RNAcentral

A comprehensive database of non-coding RNA sequences that provides a single access point to RNA sequences from a range of resources.


dictyBase

The central resource for Dictyostelid genomics, providing model organism database services for the research community.


Community Assessment of Community Annotation with Ontologies

A collaborative annotation project where undergraduate students use the Gene Ontology to annotate proteins based on evidence from scientific papers.


GO Central

The core GO Consortium annotation team responsible for producing annotations for a range of model organisms.


Gene Ontology Consortium

The consortium that develops and maintains the Gene Ontology and produces GO annotations based on published experimental results.


DisProt

A database of intrinsically disordered proteins that provides manually curated annotations for regions of disorder in proteins.


Alliance of Genome Resources (AGR Knowledgebase)


https://ctti-clinicaltrials.org/our-work/quality/state-of-clinical-trials/ Researchers can use CTTI’s Aggregate Analysis of ClinicalTrial.gov (AACT) database to easily access and analyze data from the ClinicalTrials.gov registry to evaluate studies and characterize the current state of clinical trials.


Answer coalesce

Answer coalesce: This service accepts a TRAPI 1.1 object containing answers and returns answers that have been coalesced by property, graph or ontology analysis.


ARAGORN

ARAGORN: Performs a query operation which compiles data from numerous ARAGORN ranking agent services.


ARAGORN Ranker

ARAGORN Ranker: The ranker used by the ARAGORN ARA, which takes a TRAPI 1.0 message containing answers, and calculates numerical scores for each answer.


ARAX Translator Reasoner

TRAPI 1.1 endpoint for the NCATS Biomedical Translator Reasoner called ARAX


Anatomical Therapeutic Chemical (ATC) Codes (from UMLS)


Automat RENCI SRI Reference KG

A graph based on the [Monarch API (https://api.monarchinitiative.org/)](https://api.monarchinitiative.org/).


Automat Chemical normalization (trapi v-1.1.0)

A graph  linking together similar compounds.  Two compounds are linked by an edge in the graph if they are equivalent when charge, salts, and stereochemistry are ignored.


Automat Chembio

A graph based on [chem2bio2rdf (http://cheminfov.informatics.indiana.edu:8080/c2b2r/)](http://cheminfov.informatics.indiana.edu:8080/c2b2r/).


Automat Cord19

A literature co-occurence graph based on parsing the CORD-19 paper set.


Automat Cord19 Scibite (trapi v-1.1.0)

A literature co-occurence graph based on the [scibite parsing (https://github.com/SciBiteLabs/CORD19)](https://github.com/SciBiteLabs/CORD19) of the CORD-19 paper set.


Automat Cord19 Scigraph (trapi v-1.1.0)

A literature co-occurence graph based on scigraph parsing of the CORD-19 paper set. All triples contain covid-19 as either subject or object.


Automat Covid Phenotypes (trapi v-1.1.0)

A hand-knowledge_assertion graph of phenotypes of covid-19.


Automat Covidkop KG (trapi v-1.1.0)

Knowledge graph constructed from Robokop KG by incorporating Cord-19 dataset and other covid related knowledge sources.


Automat CAM-KP

TRAPI interface to database of Causal Activity Models


Automat CTD

A graph based on the [Comparative Toxicogenomics Database (ctdbase.org)](ctdbase.org).


Automat DrugCentral

A graph based on DrugCentral


Automat Foodb

A graph of the food/chemical relationships in [foodb.ca](foodb.ca).


Automat GTEx

A graph containing eqtl and sqtl information from [GTEx Portal (https://gtexportal.org/home/)](https://gtexportal.org/home/). Also includes genes that the variants lie within or near.


Automat GtoPdb

A graph based on the [IUPHAR Guide to Pharmacology (https://www.guidetopharmacology.org/)](https://www.guidetopharmacology.org/)


Automat GWAS Catalog

A graph based on the GWAS Catalog


Automat Hetio

A graph based on [hetionet (het.io)](het.io).


Automat HGNC

Gene families from [HGNC (genenames.org)](genenames.org).


Automat HMDB

A graph based on the [Human Metabolome DataBase (hmdb.org)](hmdb.org).


Automat Human GOA

Human Gene Ontology Annotations from the GO consortium.


Automat IntAct

Molecular (Gene-Gene) interactions from EBI IntAct (https://www.ebi.ac.uk/intact/)](https://www.ebi.ac.uk/intact/).


Automat KEGG

A graph based on the [Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/)](https://www.genome.jp/kegg/).


Automat Monarch Initiative

The Monarch Knowledge Graph is a reference implementation of the Biolink model specification.  It contains data from the Monarch Initiative aggregated database as well as several OBO ontologies.


Automat MyChem (trapi v-1.1.0)

A graph integrating DrugBank, DrugCentral, and Aeolus data as provided by [mychem.info](mychem.info).


Automat Ontological Hierarchy (trapi v-1.1.0)

A graph for ontological hierarchy extracted from Uberongraph.


Automat Openhealth Data at Carolina

A graph based on infores:openhealthdata-carolina, providing access to counts and frequencies of conditions, procedures, drug exposures, and patient demographics, and the co-occurrence frequencies between them.


Automat PANTHER

A graph of gene families and pathways from [Panther (pantherdb.org)](pantherdb.org)


Automat Pharos

A graph based on [Pharos (pharos.nih.gov)](pharos.nih.gov).


Automat ROBOKOP KG

Biomedical Knowledge graph build by constructing relationships from federated data sets.


Automat Textmining KP

A literature co-occurrence graph created by the Translator Text Mining KP.


Automat STRING

The Search Tool for the Retrieval of INteracting Genes/proteins (STRING) database provides information on known and prediction protein-protein interactions (both direct and indirect) derived from genomic context predictions, high-throughput laboratory experiments, conserved co-expression, automated text mining, and aggregated knowledge from primary data sources.


Automat SRI Reference Knowledge Graph

The SRI reference KG aims to aggregate knowledge sources across translator using KGX.  The initial graph contains data files provided by the Monarch Initiative and several ontologies.


Automat Ubergraph

A graph representation of Ubergraph, an integration of ontologies including GO, CHEBI, Uberon, and HPO.


Automat Ubergraph Nonredundant

A graph representation of Ubergraph, an integration of ontologies including GO, CHEBI, Uberon, and HPO. The redundant version of Ubergraph contains the complete inference closure for all subclass and existential relations, including transitive, reflexive subclass relations.


Automat Viral Proteome

A graph consisting of viral proteins from UniProt, connected by similarity edges from UniRef.


Automat Multiomics EHRMLA May Treat API

A graph consisting of May Treat associations from Multiomics Electronic-Health-Record (EHR) Machine Learning Analysis (MLA) using the Providence health records


Automat Multiomics EHRMLA Clinical Connections API

A graph consisting of clinical connections associations from Multiomics Electronic-Health-Record (EHR) Machine Learning Analysis (MLA) using the Providence health records


BiGG Models

a knowledgebase of genome-scale metabolic network reconstructions


BindingDB

BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. As of July 31, 2021, BindingDB contains 41,300 Entries, each with a DOI, containing 2,303,972 binding data for 8,561 protein targets and 995,797 small molecules.


The Biological General Repository for Interaction Datasets


BioLink API

API integration layer for linked biological objects.


Biolink Model Lookup

Biolink Model Lookup service.


National Center for Biomedical Ontology BioPortal


Big GIM 1 API

Documentation of the Big GIM 1 KP query web services.


BioThings DGIdb API

Documentation of the BioThings DGIdb query web services.


BioThings DISEASES API

Documentation of the DISEASES query web services.


BioThings EBIgene2phenotype API

Documentation of the EBIgene2phenotype query web services.


BioThings Gene Ontology Biological Process API

Documentation of the Gene Ontology Biological Process query web services.


BioThings Gene Ontology Cellular Component API

Documentation of the Gene Ontology Cellular Component query web services.


BioThings Gene Ontology Molecular Activity API

Documentation of the Gene Ontology Molecular Activity query web services.


BioThings Human Phenotype Ontology API

Documentation of the HPO query web services.


BioThings MGIgene2phenotype API

Documentation of the MGIgene2phenotype query web services.


Multiomics BigGIM-DrugResponse KP API

Documentation of the Drug Response KP query web services.

infores:biogrid infores:huri infores:gtex infores:ttd infores:tcga infores:gdsc


Multiomics EHR Risk KP API

Documentation of the Multiomics Electronic-Health-Record (EHR) Risk KP query web services.


Multiomics Pharmacogenomics KP API

Documentation of the Pharmacogenomics KP query web services.

infores:drugbank infores:ncbi-gene infores:hpo infores:hpo-annotations infores:sider infores:mondo infores:drugcentral infores:pharmgkb infores:primekg infores:cellmarker infores:signor


Providence St. Joseph EHR Data

A partnership with Providence/Swedish Health Services and Institute for Systems Biology allows analysis of 26 million EHRs from patients in seven states in the US, including Alaska, California, Montana, Oregon, Washington, Texas, and New Mexico. Please email data-access@isbscience.org for more information.


Multiomics EHRMLA May Treat API

Documentation of the Multiomics Electronic-Health-Record (EHR) Machine Learning Analysis (MLA) May Treat query web services.


Multiomics EHRMLA Clinical Connections API

Documentation of the Multiomics Electronic-Health-Record (EHR) Machine Learning Analysis (MLA) Clinical Connections query web services.


Multiomics Wellness KP API

Documentation of the Multiomics Wellness KP query web services.


Multiomics ClinicalTrials KP API

infores:aragorn infores:arax infores:rtx-kg2 infores:service-provider-trapi


BioThings PFOCR API

Documentation of the pfocr query web services.


BioThings SEMMEDDB API

Documentation of the BioThings SEMMEDDB query web services.


SEMMED Anatomy API

Documentation of the SEMMED disease query web services.  Learn more about [mydisease.info](http://pending.biothings.io/semmed)


SEMMED Disease API

Documentation of the SEMMED disease query web services.  Learn more about [semmed disease](http://pending.biothings.io/semmed)


Multiomics TCGA Mutation Frequency KP API

Documentation of the TCGA Mutation Frequency KP query web services.


BioThings UBERON Ontology API

Documentation of the UBERON query web services.


BioThings Rhea API

Documentation of the BioThings Rhea query web services.


BioThings BioPlanet Pathway-Disease API

Documentation of the BioThings [BioPlanet](https://tripod.nih.gov/bioplanet/#) pathway-disease association query web services.


BioThings BioPlanet Pathway-Gene API

Documentation of the BioThings [BioPlanet](https://tripod.nih.gov/bioplanet/#) pathway-gene association query web services.


BioThings BindingDB API

Documentation of the BioThings [BindingDB](https://www.bindingdb.org/rwd/bind/index.jsp) query web services.


DailyMed

The DailyMed database contains labeling, submitted by companies to the Food and Drug Administration (FDA).


C. elegans Gross Anatomy Ontology

A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.


C. elegans phenotype

A structured controlled vocabulary of Caenorhabditis elegans phenotypes


CAM-KP API

TRAPI interface to database of Causal Activity Models


Chemical Entity of Biological Interest

a freely available dictionary of molecular entities focused on ‘small’ chemical compounds


ChemBank

Initiative for Chemical Genetics contract from the National Cancer Institute


ChEMBL

a manually knowledge_assertion database of bioactive molecules with drug-like properties.


Clinital Interpretation of Variants in Cancer


Clinical Genome Resource (ClinGen)

ClinGen is a NIH-funded resource dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research


ClinVar

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence.


Connectivity Map

genome-scale library of cellular signatures that catalogs transcriptional responses to chemical, genetic, and disease perturbation"'


Columbia Clinical Data Warehouse for Health Patient EHR Data

The Columbia Clinical Data Warehouse (CDW) contains clinical information for over 4.5 million individuals treated at Columbia University Irving Medical Center (CUIMC) since the 1980s.


Columbia Open Health Data (COHD)

The Columbia Open Health Data (COHD) API provides access to counts and frequencies (i.e., EHR prevalence) of conditions, procedures, drug exposures, and patient demographics, and the co-occurrence frequencies between them. Count and frequency data were derived from the [Columbia University Medical Center''s](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient and outpatient data. Counts are the number of patients associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or who had a procedure. Frequencies are the number of unique patients associated with the concept divided by the total number of patients in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution.           Four datasets are available:  1) 5-year non-hierarchical dataset: Includes clinical data from 2013-2017   2) lifetime non-hierarchical dataset: Includes clinical data from all dates   3) 5-year hierarchical dataset: Counts for each concept include patients from descendant concepts. Includes clinical data from 2013-2017. 4) BETA! Temporal co-occurrence data  In the 5-year hierarchical data set, the counts for each concept include the patients from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes patients with Ibuprofen 600 MG Oral Tablet (ID 19019073 patients), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc.   While the lifetime dataset captures a larger patient population and range of concepts, the 5-year dataset has better underlying data consistency.   Clinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO).    The following resources are available through this API:    1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc.    2. OMOP: Access to the common vocabulary for name and concept identifier mapping   3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of patients with the code(s) / total number of patients.    4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency.    A [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.   COHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (Red Team). This work was supported in part by grants: NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.  The following external resources may be useful:   [OHDSI](https://www.ohdsi.org/)   [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki)   [Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy)   [Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets)

infores:aragorn infores:arax infores:openpredict infores:service-provider-trapi


The Columbia Open Health Data (COHD) for COVID-19 Research API provides access to counts and frequencies (i.e., EHR visit prevalence) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them for a cohort of hospitalized COVID-19 patients and two comparator cohorts of hospitalized influenza patients and hospitalized patients. Count and frequency data were derived from the [Columbia University Medical Center''s](http://www.cumc.columbia.edu/) [OHDSI](https://www.ohdsi.org/) database including inpatient. Counts are the number of inpatient visits associated with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of unique visits associated with the concept divided by the total number of visits in the dataset, i.e., prevalence in the electronic health records. To protect patient privacy, all concepts and pairs of concepts where the count <= 10 were excluded, and counts were randomized by the Poisson distribution.           Datasets from three primary cohorts are available:  1) COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+). 2) General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019. 3) Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.  Both hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc.   Clinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki). API methods are provided to map to/from other vocabularies supported in OMOP and other ontologies using the EMBL-EBI Ontology Xref Service (OxO).    The following resources are available through this API:    1. Metadata: Metadata on the COHD database, including dataset descriptions, number of concepts, etc.    2. OMOP: Access to the common vocabulary for name and concept identifier mapping   3. Clinical Frequencies: Access to the counts and frequencies of conditions, procedures, and drug exposures, and the associations between them. Frequency was determined as the number of visits with the code(s) / total number of visits.    4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency.    A [Python notebook](https://github.com/WengLab-InformaticsResearch/cohd_api/blob/master/notebooks/COHD_API_Example.ipynb) demonstrates simple examples of how to use the COHD API.   COHD was developed at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (TReK Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.  The following external resources may be useful:   [OHDSI](https://www.ohdsi.org/)   [OMOP Common Data Model](https://github.com/OHDSI/CommonDataModel/wiki)   [Athena](http://athena.ohdsi.org) (OMOP vocabularies, search, concept relationships, concept hierarchy)   [Atlas](http://www.ohdsi.org/web/atlas/) (OMOP vocabularies, search, concept relationships, concept hierarchy, concept sets)    [NCATS Biomedical Data Translator](https://sites.google.com/ncats.nih.gov/translator-io/home)


Columbia Open Health Data for COVID-19 Research API


Connections Hypothesis Provider API

A Translator Reasoner API for the Connections Hypothesis Provider


Current Procedural Terminology (CPT) Codes (from UMLS)


Translator knowledge_assertion Query Service

The Translator Curated Query Service (CQS) is an SRI service that provides ARA-like capabilities. The service generates ‘predicted’ edges in response to inferred queries, based on customizable inference rules that are captured as CQS templates. The CQS links predictions to their supporting aux graphs and attaches provenance metadata, and then scores the results.

infores:automat-icees-kg infores:automat-cohd infores:automat-isb-EHRMLA-data infores:connections-hypothesis infores:multiomics-ctkp infores:text-mining-provider-targeted infores:service-provider-tmkp-targeted infores:openpredict infores:service-provider-aeolus infores:spoke-chembl infores:molepro-chembl infores:rtxkg2-semmed infores:service-provider-semmed infores:service-provider-chembl infores:cam-kp


Comparative Toxicogenomics Database

A robust, publicly available database that aims to advance understanding about how environmental exposures affect human health.


Cancer Therapeutics Response Portal

links genetic, lineage, and other cellular features of cancer cell lines to small-molecule sensitivity with the goal of accelerating discovery of patient-matched cancer therapeutics.


Drugs to target pAthways by the Tissue Expression


Cancer Dependency Map

Cancer Dependency Map to systematically identify genetic and pharmacologic dependencies and the biomarkers that predict them.


Drug Gene Interaction Database

information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data are normalized and merged into conceptual groups.


Drug-Induced Liver Injury Network (DILIN) Participant Data


FDA Adverse Event Reporting System

The FDA Adverse Event Reporting System (FAERS) is a database that contains information on adverse event and medication error reports submitted to FDA.


Drosophila gross anatomy

An ontology representing the gross anatomy of Drosophila melanogaster.


DISEASES

DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations  from automatic text mining, manually curated literature, cancer mutation data, and  genome-wide association studies. We further unify the evidence by assigning confidence  scores that facilitate comparison of the different types and sources of evidence.


Disease Ontology Annotation Framework (DOAF)


Database of knowledge_assertion Mutations


Drug Repurposing Hub

knowledge_assertion and annotated collection of FDA-approved drugs, clinical trial drugs, and pre-clinical tool compounds with a companion information resource


DrugBank

A comprehensive, free-to-access, online database containing information on drugs and drug targets. As both a bioinformatics and a cheminformatics resource, we combine detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information

infores:molepro infores:openpredict infores:rtx-kg2 infores:catrax-pharmacogenomics


DrugCentral

Online drug information resource created and maintained by Division of Translational Informatics at University of New Mexico in collaboration with the IDG.

infores:molepro infores:mychem-info infores:rtx-kg2 infores:catrax-pharmacogenomics


DrugMechDB

A database of paths that represent the mechanism of action from a drug to a disease in an indication.


European Bioinformatics Institute Gene to Phenotype Resource


EBI Proteins API

The Proteins REST API provides access to key biological data from UniProt and data from Large Scale Studies (LSS) mapped to UniProt. The services provide sequence feature annotations from UniProtKB, variation data from UniProtKB and mapped from LSS (1000 Genomes, ExAC, ClinVar, TCGA, COSMIC, TOPMed and gnomAD), proteomics data mapped from MS-proteomics repositories (PeptideAtlas, MaxQB, EPD and ProteomicsDB), antigen sequences mapped from Human Protein Atlas (HPA), proteomes and taxonomy search and retrieval, reference genome coordinate mappings and data from UniParc. Go to https://www.ebi.ac.uk/proteins/api/doc/ to learn more."'


QuickGO API

The QuickGO REST API provides access to key biological data from QuickGO and GOA. The services provide a unified interface to query information about ontology terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene Ontology annotations from the EBI''s GOA database, and gene products (proteins from UniProt, RNA from RNAcentral and complexes from ComplexPortal).


Environmental conditions, treatments and exposures ontology


eRAM: encyclopedia of rare disease annotations for precision medicine


Evolutionary Rate Covariation (ERC) Analysis


Explanatory Agent API

A Translator Reasoner API for the Explanatory Agent


Foundational Model of Anatomy Ontology (FMA -- both from UMLS and from OBO)


National Cancer Institute Genomic Data Commons Data Portal


The Gene Curation Coalition (GenCC)

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases


GenDR Database of Dietary Restriction-Related Genes


Genebass: Gene-based association summary statistics

Genebass is a resource of exome-based association statistics, made available to the public. The dataset encompasses 3,817 phenotypes with gene-based and single-variant testing across 281,852 individuals with exome sequence data from the UK Biobank.


GeneProf

underlying resource is throwing 404 error atm


Genetics KP

TRAPI 1.1 endpoint for the NCATS Biomedical Translator Genetics Data KP

infores:clingen infores:clinvar infores:gencc infores:genebass


Global Network of Biomedical Relationships


Gene Ontology

infores:biothings-go-bp infores:biothings-go-cc infores:biothings-go-mf infores:ebi-quick-go infores:rtx-kg2


Gene Ontology Causal Activity Model Annotations


Adverse Outcome Pathways Casual Activity Models


GOTE (Gpcrs to dOwnstream cellular pathways byTissue Expression)


Guide to Pharmacology

An expert-knowledge_assertion resource of ligand-activity-target relationships, the majority of which come from high-quality pharmacological and medicinal chemistry literature


Healthcare Common Procedure Coding System (from UMLS)


HCPCS Version of Current Procedural Terminology (HCPT) (from UMLS)


Human Metabolome Database

A freely available electronic database containing detailed information about small molecule metabolites found in the human body


Human Protein Atlas

The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.


ICEES (Integrated Clinical and Environmental Exposures Service)

Information Resource


integrated Dietary Supplement Knowledge Base


imProving Agent

imProving Agent OpenAPI TRAPI Specification


OpenAPI for indigo NCATS Biomedical Translator Reasoner


Inxight: Drugs

NCATS Inxight Drugs contains information on ingredients in medicinal products, including: US APPROVED DRUGS, MARKETED DRUGS and INVESTIGATIONAL DRUGS. Manually knowledge_assertion data supplied by the FDA and private companies, and provides marketing and regulatory status, rigorous drug ingredient definitions, biological activity, clinical use, and more.


iPTMNet

A bioinformatics resource for integrated understanding of protein post-translational modifications (PTMs)  in systems biology context. It connects multiple disparate bioinformatics tools and systems text mining,  data mining, analysis and visualization tools, and databases and ontologies into an integrated  cross-cutting research resource to address the knowledge gaps in exploring and discovering PTM networks.


Institute for Systems Biology COVID-19 Immune Response Study


Institute for Systems Biology Scientific Wellness


Kyoto Encyclopedia of Genes and Genomes (KEGG)


KinAce

https://kinace.kinametrix.com/#section-about The KinAce web portal aggregates and visualizes the network of interactions between protein-kinases and their substrates in the human genome.  To begin, click on one of the tabs above. Each tab provides a unique way to select a set of proteins and display the known kinase-substrate interactions between them.


Translator Knowledge Collaboratory API

Translator Reasoner API for the Knowledge Collaboratory,hosted on the [Nanopublications network](https://nanopub.net/), for annotated drug  indications or any other BioLink-compliant claims. This Open API supports [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI) queries and the [`KGX`](https://github.com/biolink/kgx) format   See the API GitHub repository: https://github.com/MaastrichtU-IDS/knowledge-collaboratory-api This service is supported by the [NCATS Translator project](https://ncats.nih.gov/translator/about)'


Library of Integrated Network-Based Cellular Signatures


LitVar API

LitVar allows the search and retrieval of variant relevant information from the biomedical literature and shows key biological relations between a variant and its close related entities (e.g. genes, diseases, and drugs). The LitVar results are automatically extracted (with regular updates) from over 27 million PubMed articles as well as applicable full-text articles in PubMed Central.


Logical Observation Identifiers Names and Codes


Mammalian Phenotype Ontology

Standard terms for annotating mammalian phenotypic data.


Medical Action Ontology

see also https://github.com/monarch-initiative/MAxO


Medication Reference Terminology (MED-RT) (from UMLS)


Mouse Developmental Anatomy Ontology

An ontology for mouse anatomy covering embryonic development and postnatal stages.


Mouse pathology ontology

A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes


Molecular Interactions Controlled Vocabulary


Molecular Data Provider for NCATS Biomedical Translator Reasoners

infores:bigg-models infores:bindingdb infores:chebi infores:chembank infores:chembl infores:cmap infores:ctd infores:ctrp infores:depmap infores:dgidb infores:drug-repurposing-hub infores:drugbank infores:drugcentral infores:dsstoxdb infores:gelinea infores:genetics-data-provider infores:gtopdb infores:hgnc infores:hmdb infores:inxight-drugs infores:kinomescan infores:molepro infores:msigdb infores:pharmgkb infores:pharos infores:probe-miner infores:pubchem infores:reactome infores:rxnorm infores:sider infores:sri-node-normalizer infores:stitch infores:string infores:uniprot

infores:aragorn infores:arax infores:molepro infores:service-provider-trapi


MyChem.info API

Documentation of the MyChem.info chem query web services.  Learn more about [MyChem.info](http://MyChem.info/)

infores:aeolus infores:chebi infores:chembl infores:drugcentral infores:fda-orphan-drug-db


MyDisease.info API

Documentation of the MyDisease.info disease query web services.  Learn more about [mydisease.info](http://mydisease.info/)

infores:ctd infores:disgenet infores:hpo-annotations infores:mondo


MyGene.info API

Documentation of the MyGene.info Gene Query web services. Learn more about [MyGene.info](http://mygene.info/)

infores:clingen infores:cpdb infores:ncbi-gene infores:panther infores:reactome


MyVariant.info API

Documentation of the MyVariant.info Variant Query web services. Learn more about [MyVariant.info](http://myvariant.info/)


National Center for Advancing Translational Science Biomedical Data Translator Autonomous Relay System

NCATS Translator Autonomous Relay System Translator  Autonomous Relay System


National Center for Biotechnology Information Gene


North Carolina Department of Environmental Quality Concentrated Animal Feeding Operations Exposures Data


North Carolina Department of Environmental Quality Landfill Exposures Data


National Drug Data File (NDDF) (from UMLS)


National Drug File - Reference Terminology (NDF-RT) (from UMLS)


NIEHS Environmental Polymorphisms Registry


Open Health Data @ Carolina

OHD@Carolina, Open Health Data @ Carolina

Open Health Data @ Carolina provides access to counts and frequencies (i.e., EHR prevalence) of conditions, procedures, drug exposures, and patient demographics, and the co-occurrence frequencies between them. Count and frequency data were derived from UNC Health's OMOP database on a five-year cohort (~6M patients over years 2018 through 2022) of all UNC Health patients,  including their inpatient and outpatient visit data. Counts represent the number of  patients associated with a given concept, e.g., diagnosed with a condition,  exposed to a drug, or who had a procedure. Frequencies are the number of unique patients associated with the concept divided by the total number of patients in the dataset,  i.e., prevalence in the electronic health records. To protect patient privacy,  all concepts and pairs of concepts where the count was <= 10 were excluded,  and counts were randomized by the Poisson distribution.


Ontology Lookup Service API

The OLS REST API provides access to key biological data from OLS. The services provide a unified interface to query information about ontology terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene Ontology annotations from the EBI's GOA database, and gene products (proteins from UniProt, RNA from RNAcentral and complexes from ComplexPortal).


Online Mendelian Inheritance in Man (OMIM)


Observational Medical Outcomes Partnership Common Data Model


Observational Medical Outcomes Partnership Observational Health Data Sciences and Informatics API


Phenomics Integrated Ontology

An ontology for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.


Pathosystems Resource Integration Center


Text Mined pharmacogenomic polymorphisms

Text mined pharmacogenomic polymorphisms to assist curation of PharmGKB.


Psychoactive Drug Screening Program

This service provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters.


Pfam

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).  Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function.  Pfam also generates higher-level groupings of related entries, known as clans. A clan is a collection of Pfam entries which are related by similarity of sequence, structure or profile-HMM.  The data presented for each entry is based on the UniProt Reference Proteomes but information on individual UniProtKB sequences can still be found by entering the protein accession. Pfam full alignments are available from searching a variety of databases, either to provide different accessions (e.g. all UniProt and NCBI GI) or different levels of redundancy.


Pharos

focusing on three of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs, Ion channels (ICs), Kinases


PhosphoSitePlus

provides comprehensive information and tools for the study of protein  post-translational modifications (PTMs) including phosphorylation, acetylation, and more.


PrimeKG, Precision Medicine Knowledge Graph


Psychological Index Terms (PSY) (from UMLS)


PubChem

an open chemistry database at the National Institutes of Health (NIH), mostly contains small molecules, but also larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules


RGD API

The RGD API


ROBOKOP

An API for answering biomedical questions


ROBOKOP (Reasoning Over Biomedical Objects linked in Knowledge-Oriented Pathway)


RTX KG2

TRAPI 1.1 endpoint for the NCATS Biomedical Translator KP called RTX KG2


RxNorm

normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, and Gold Standard Drug Database


SABIO-RK Biochemical Reaction Kinetics Database


Semantic Analytics & Clean Data Intelligence Experts


SmartAPI API

This is the API provided from SmartAPI, https://smart-api.info, application.


SnpEff

Genetic variant annotation and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).


SPOKE KP

SPOKE KP - an NIH NCATS Knowledge Provider to expose UCSFs SPOKE

infores:bgee infores:bindingdb infores:gdsc infores:chembl infores:civic infores:lincs infores:disease-ontology infores:diseases infores:drugcentr infores:fooddb infores:gwas-catalog infores:hpa infores:interpro infores:kegg infores:go infores:mesh infores:ncbi-taxonomy infores:omim infores:path-pheno-db infores:pfam infores:sider infores:string infores:uberon infores:uniprot


Edge Normalization Service

SRI service to validate and normalize edges to Translator standards.


Name Resolver

Service to resolve Translator concept names.


Node Normalization

Node normalization takes a CURIE, and returns resolved alias and the canonical identifier of a node.


Ontology-KP API

TRAPI interface to integrated ontology knowledgebase


SRI Reference Knowledge Graph API

The SRI reference KG aims to aggregate knowledge sources across translator using KGX.  The initial graph contains data files provided by the Monarch Initiative and several ontologies.


SRI SemMedDb KGX File Set

The SRI Semantic Medline Database is a Biolink Model compliant KGX file set mapping of NIH NLM SemMedDb.  The graph contains data files generated by the ETL process pipeline at https://github.com/NCATS-Tangerine/semmed-biolink. The KGX file set is hosted on the Knowledge Graph Exchange Archive (https://archive.translator.ncats.io).


STITCH

Database of known and prediction interactions between chemicals and proteins. The interactions include direct (physical) and indirect (functional) associations


Strider

Translator Autonomous Relay Agent


Search Tool for the Retrieval of Interacting Genes/Proteins


Target Illumination GWAS Analytics

Aggregating and assessing experimental evidence for interpretable, explainable, accountable gene-trait associations.


Text Mining COOCCURRENCE API

API serving a knowledge graph comprised of pairs of concepts that have been found to co-occur in the scientific literature. Here, cooccurrence of a pair of biomedical concepts within a single document or sentence serves as a proxy for a potential relationship between the two concepts.


Text Mining Targeted Association API

API serving explicitly targeted Biolink Associations extracted from sentences in the scientific literature. Here, targeted refers to the fact that this service is based on text-mining models targeted to extract specific associations between concepts, as opposed to concepts cooccurring with each other.


NHLBI Trans-Omics for Precision Medicine


Therapeutic Target Database (TTD)

TTD is a database providing information about the known and explored therapeutic protein  and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs  directed at each of these targets.


Ubergraph

A graph representation of Ubergraph, an integration of ontologies including GO, CHEBI, Uberon, and HPO.


UNC Carolina Data Warehouse for Health Patient EHR Data


Unsecret Agent OpenAPI for NCATS Biomedical Translator Reasoners


United States Census Bureau American Community Survey Data


United States Census Bureau TIGER/line Roadway Data


United States Department of Transportation Roadway Exposures Data


United States Environmental Protection Agency Airborne Pollutant Exposures Data


Unified phenotype ontology

The uPheno ontology integrates multiple phenotype ontologies into a unified cross-species phenotype ontology.


Veterans Association National Drug File (VANDF) (from UMLS)


WikiPathways

WikiPathways is an open science platform for biological pathways contributed, updated, and used by the research community.


Xenopus Phenotype Ontology

XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and tropicalis.


Translator Workflow Runner

Translator general purpose workflow runner


Zebrafish anatomy and development ontology

A structured controlled vocabulary of the anatomy and development of the Zebrafish


DDinter

DDInter is an open-access database specific to drug-drug interactions with annotations including mechanism description, risk levels, management strategies, alternative medications, etc. to improve clinical decision-making and patient safety.


Ki database

The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at UNC's Psychoactive Drug Screening Program


Community Structure-Activity Resource

CSAR disseminated experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes


Drug Design Data Resource

The Drug Design Data Resource (D3R) aims to advance the technology of computer-aided drug discovery through the interchange of high quality protein-ligand datasets


Adverse Event Open Learning through Universal Standardization (AEOLUS)

A knowledge_assertion and standardized version of FAERS removing duplicate case records, applying standardized vocabularies with drug names mapped to RxNorm concepts and outcomes mapped to SNOMED-CT concepts, and pre-computed summary statistics about drug-outcome relationships for general consumption.


Richards Effector Gene List

An effector index to predict target genes at GWAS loci


The Human Reference Protein Interactome Mapping Project

A human ‘all-by-all’ reference interactome map of human binary protein interactions, or ‘HuRI’. With approximately 53,000 protein–protein interactions, HuRI has approximately four times as many such interactions as there are high-quality knowledge_assertion interactions from small-scale studies


Zebrafish Phenotype Ontology

The Zebrafish Phenotype Ontology formally defines all phenotypes of the Zebrafish model organism.


FlyBase

A Database of Drosophila Genes & Genomes


Xenbase

Xenbase's mission is to provide the international research community with a comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research. Xenbase also provides a critical data sharing infrastructure for many other NIH-funded projects, and is a focal point for the Xenopus community. In addition to our primary goal of supporting Xenopus researchers, Xenbase enhances the availability and visibility of Xenopus data to the broader biomedical research community.


BioThings RARe-SOURCE API

Documentation of the BioThings API for [NCATS RARe-SOURCE](https://raresource.nih.gov/) data.


NCATS RARe-SOURCE

Integrated Bioinformatics Resource for Rare Diseases


BioThings SuppKG API

Documentation of the BioThings API for [SuppKG](https://github.com/zhang-informatics/SemRep_DS/tree/main/SuppKG) data. SuppKG contains relations between dietary supplements and other entities, such as diseases. More information can be found in [this  paper](https://doi.org/10.1016/j.jbi.2022.104120).


SuppKG

SuppKG contains relations between dietary supplements and other entities, such as diseases.  More information can be found in [this paper](https://doi.org/10.1016/j.jbi.2022.104120).


BioThings DDInter API

Documentation of the BioThings API for [DDInter](http://ddinter.scbdd.com/) data.


BioThings GTRx API

Documentation of the BioThings API for [Genome-to-Treatment (GTRx™)](https://gtrx.rbsapp.net/about.html).  This API includes the content from the linked website, specifically the recommended acute treatments and  interventions for seriously ill newborns, infants and children with newly diagnosed genetic diseases.  These may include therapeutics, dietary changes, surgery, medical devices or other interventions.  For more info, see the paper (open-access): https://www.nature.com/articles/s41467-022-31446-6.


Biothings Therapeutic Target Database API

Documentation of the BioThings API for [TherapeuticTargetDatabase](https://db.idrblab.net/ttd/). This KP contains drug-disease, target-disease, drug-protein target, and biomarker-disease associations.


RaMPDB

RaMP-DB (Relational database of Metabolomic Pathways) is a multi-sourced integrated database with comprehensive annotations on biological pathways, structure/chemistry, disease and ontology annotations for genes, proteins, and metabolites. RaMP-DB also provides a framework for single and batch queries of those annotations, and for performing chemical and biological pathway enrichment analyses on input multi-omic datasets.


BioThings AGR API

Documentation of the BioThings API for [AGR](https://www.alliancegenome.org/downloads) disease associations data.


InnateDB

InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions  and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection.  The database captures an improved coverage of the innate immunity interactome by integrating known interactions  and pathways from major public databases together with manually-curated data into a centralised resource.


BioThings InnateDB API

Documentation of the BioThings API for [InnateDB](https://www.innatedb.com/) data.


iPTMnet

iPTMnet is a bioinformatics resource for integrated understanding of protein post-translational modifications (PTMs) in systems biology context. It connects multiple disparate bioinformatics tools and systems text mining, data mining, analysis and visualization tools, and databases and ontologies into an integrated cross-cutting research resource to address the knowledge gaps in exploring and discovering PTM networks.


FDA Orphan Drug Project designation database

Resource for searching FDA Orphan Drug Designations and Approvals


Complex Portal

The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes  from a number of key model organisms. The majority of complexes are made up of proteins but  may also include nucleic acids or small molecules. All data is freely available for search  and download


BioThings repoDB API

Documentation of the BioThings API for [repoDB](https://unmtid-shinyapps.net/shiny/repodb/) data.  and download


BioThings HMDB API

Documentation of the BioThings API for [HMDB](https://hmdb.ca/) data.


FoodData Central

FoodData Central is an integrated data system that provides expanded nutrient profile data  and links to related agricultural and experimental research.


BioThings FoodData Central API

Documentation of the BioThings API for  [FoodData Central](https://fdc.nal.usda.gov/index.html) data.


BioThings FooDB API

Documentation of the BioThings API for [FooDB](https://foodb.ca/) data.


TISSUES

TISSUES is a weekly updated web resource that integrates evidence on tissue expression  from manually curated literature, proteomics and transcriptomics screens, and automatic  text mining. We map all evidence to common protein identifiers and Brenda Tissue Ontology  terms, and further unify it by assigning confidence scores that facilitate comparison of  the different types and sources of evidence. We finally visualize these scores on a  schematic human body to provide a convenient overview.


BioThings TISSUES API

Documentation of the BioThings API for [TISSUES](https://tissues.jensenlab.org/About) data.


MyGeneset.info API

MyGeneset allows scientists to conveniently collect, save, and share sets of genes  from thousands of different species.


infores:aragorn infores:arax infores:biothings-explorer infores:improving-agent infores:unsecret-agent


Annotator Service

Service to provide detailed annotations for any given biomedical entities.


PhenoPacket Store

A repository for storage and retrieval of phenopackets, which are structured data  for representing and exchanging phenotypic information across computational contexts.


The Amyloidoses Collection (AmyCo) Database

The Amyloidoses Collection (AmyCo) database contains manually curated data from articles on amyloidoses and other diseases related to amyloid deposition. The resource is not directly  accessible at this time, but Jensen Lab's [DISEASES](https://doi.org/10.1093/database/baac019) reports that it ingests this resource.