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infores_catalog.yaml
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infores_catalog.yaml
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---
information_resources:
- id: infores:agrkb
status: released
name: Alliance of Genome Resources (AGR Knowledgebase)
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Alliance-of-Genome-Resources
synonym:
- ALLIANCE
knowledge level: curated
agent type: not_provided
- id: infores:aact
status: released
name: Aggregate Analysis of ClinicalTrial.gov (AACT) database
xref:
- https://aact.ctti-clinicaltrials.org/
synonym:
- AACT
knowledge level: curated
agent type: not_provided
description: 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.
- id: infores:answer-coalesce
status: deprecated
name: Answer coalesce
xref:
- https://github.com/ranking-agent/AnswerCoalesce
knowledge level: curated
agent type: not_provided
description: >-
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.
- id: infores:aragorn
status: released
name: ARAGORN
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/ARAGORN-and-ROBOKOP
knowledge level: predicted
agent type: not_provided
description: >-
ARAGORN: Performs a query operation which compiles data from numerous
ARAGORN ranking agent services.
- id: infores:aragorn-ranker
status: deprecated
name: ARAGORN Ranker
xref:
- https://github.com/ranking-agent/aragorn-ranker
synonym:
- ARAGORN
knowledge level: curated
agent type: not_provided
description: >-
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.
- id: infores:arax
status: released
name: ARAX Translator Reasoner
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Expander-Agent
synonym:
- ARAX
knowledge level: predicted
agent type: not_provided
description: TRAPI 1.1 endpoint for the NCATS Biomedical Translator Reasoner called
ARAX
- id: infores:atc-codes-umls
status: released
name: Anatomical Therapeutic Chemical (ATC) Codes (from UMLS)
xref:
- https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC/index.html
knowledge level: curated
agent type: not_provided
- id: infores:atgo
status: released
name: Autophagy Ontology
xref:
- https://pubmed.ncbi.nlm.nih.gov/28132844/
synonym:
- ATGO
knowledge level: curated
agent type: not_provided
- id: infores:athena
status: released
name: Athena
xref:
- https://athena.ohdsi.org/search-terms/start
knowledge level: curated
agent type: not_provided
- id: infores:automat-genome-alliance
status: released
name: Automat Alliance of Genome Resources
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
- id: infores:automat-renci-sri-reference-kg
status: deprecated
name: Automat RENCI SRI Reference KG
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on the [Monarch API (https://api.monarchinitiative.org/)](https://api.monarchinitiative.org/).
- id: infores:automat-chem-norm
status: deprecated
name: Automat Chemical normalization (trapi v-1.1.0)
description: >-
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.
knowledge level: curated
agent type: not_provided
- id: infores:automat-chembio
status: deprecated
name: Automat Chembio
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: >-
A graph based on [chem2bio2rdf (http://cheminfov.informatics.indiana.edu:8080/c2b2r/)](http://cheminfov.informatics.indiana.edu:8080/c2b2r/).
- id: infores:automat-cord19
status: deprecated
name: Automat Cord19
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: text_mined
agent type: not_provided
description: >-
A literature co-occurence graph based on parsing the CORD-19 paper set.
- id: infores:automat-cord19-scibite
status: deprecated
name: Automat Cord19 Scibite (trapi v-1.1.0)
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: text_mined
agent type: not_provided
description: >-
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.
- id: infores:automat-cord19-scigraph
status: deprecated
name: Automat Cord19 Scigraph (trapi v-1.1.0)
description: >-
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.
knowledge level: text_mined
agent type: not_provided
- id: infores:automat-covid-phenotypes
status: deprecated
name: Automat Covid Phenotypes (trapi v-1.1.0)
knowledge level: curated
agent type: not_provided
description: A hand-curated graph of phenotypes of covid-19.
- id: infores:automat-covidkop
status: deprecated
name: Automat Covidkop KG (trapi v-1.1.0)
knowledge level: curated
agent type: not_provided
description: >-
Knowledge graph constructed from Robokop KG by incorporating Cord-19
dataset and other covid related knowledge sources.
- id: infores:automat-cam-kp
status: released
name: Automat CAM-KP
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-CAM-AOP
knowledge level: curated
agent type: not_provided
description: TRAPI interface to database of Causal Activity Models
- id: infores:automat-ctd
status: released
name: Automat CTD
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on the [Comparative Toxicogenomics Database (ctdbase.org)](ctdbase.org).
- id: infores:automat-drug-central
status: released
name: Automat DrugCentral
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on DrugCentral
- id: infores:automat-foodb
status: released
name: Automat Foodb
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph of the food/chemical relationships in [foodb.ca](foodb.ca).
- id: infores:automat-gtex
status: released
name: Automat GTEx
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: >-
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.
- id: infores:automat-gtopdb
status: released
name: Automat GtoPdb
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on the [IUPHAR Guide to Pharmacology (https://www.guidetopharmacology.org/)](https://www.guidetopharmacology.org/)
- id: infores:automat-gwas-catalog
status: released
name: Automat GWAS Catalog
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on the GWAS Catalog
- id: infores:automat-hetio
status: deprecated
name: Automat Hetio
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on [hetionet (het.io)](het.io).
- id: infores:automat-hetionet
status: released
name: Automat Hetionet
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on [hetionet (het.io)](het.io).
- id: infores:automat-hgnc
status: released
name: Automat HGNC
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: Gene families from [HGNC (genenames.org)](genenames.org).
- id: infores:automat-hmdb
status: released
name: Automat HMDB
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on the [Human Metabolome DataBase (hmdb.org)](hmdb.org).
- id: infores:automat-human-goa
status: released
name: Automat Human GOA
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: Human Gene Ontology Annotations from the GO consortium.
- id: infores:automat-icees-kg
status: released
name: Automat ICEES KG
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-ICEES
knowledge level: correlation
agent type: not_provided
- id: infores:automat-intact
status: released
name: Automat IntAct
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: Molecular (Gene-Gene) interactions from EBI IntAct (https://www.ebi.ac.uk/intact/)](https://www.ebi.ac.uk/intact/).
- id: infores:automat-kegg
status: deprecated
name: Automat KEGG
knowledge level: curated
agent type: not_provided
description: A graph based on the [Kyoto Encyclopedia of Genes and Genomes (https://www.genome.jp/kegg/)](https://www.genome.jp/kegg/).
- id: infores:automat-mychem-info
status: deprecated
name: Automat MyChem (trapi v-1.1.0)
knowledge level: curated
agent type: not_provided
description: >-
A graph integrating DrugBank, DrugCentral, and Aeolus data as provided
by [mychem.info](mychem.info).
- id: infores:automat-ontology-hierarchy
status: deprecated
name: Automat Ontological Hierarchy (trapi v-1.1.0)
knowledge level: curated
agent type: not_provided
description: A graph for ontological hierarchy extracted from Uberongraph.
- id: infores:automat-panther
status: released
name: Automat PANTHER
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph of gene families and pathways from [Panther (pantherdb.org)](pantherdb.org)
- id: infores:automat-pharos
status: released
name: Automat Pharos
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: A graph based on [Pharos (pharos.nih.gov)](pharos.nih.gov).
- id: infores:automat-robokop-kg
status: released
name: Automat ROBOKOP KG
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: Biomedical Knowledge graph build by constructing relationships from
federated data sets.
- id: infores:automat-text-mining-provider
status: deprecated
name: Automat Textmining KP
knowledge level: curated
agent type: not_provided
description: A literature co-occurrence graph created by the Translator Text Mining KP.
- id: infores:automat-string-db
status: released
name: Automat STRING
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: >-
The Search Tool for the Retrieval of INteracting Genes/proteins (STRING)
database provides information on known and predicted 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.
- id: infores:automat-sri-reference-kg
status: released
name: Automat SRI Reference Knowledge Graph
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/SRI-Reference-Knowledge-Graph
knowledge level: curated
agent type: not_provided
description: >-
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.
- id: infores:automat-ubergraph
status: released
name: Automat Ubergraph
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: >-
A graph representation of Ubergraph, an integration of ontologies
including GO, CHEBI, Uberon, and HPO.
- id: infores:automat-ubergraph-nonredundant
status: deprecated
name: Automat Ubergraph Nonredundant
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
knowledge level: curated
agent type: not_provided
description: >-
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.
- id: infores:automat-viral-proteome
status: released
name: Automat Viral Proteome
knowledge level: curated
agent type: not_provided
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Automat
description: >-
A graph consisting of viral proteins from UniProt, connected by similarity
edges from UniRef.
- id: infores:bfo
status: released
name: Basic Formal Ontology
xref:
- http://www.obofoundry.org/ontology/bfo.html
synonym:
- BFO
knowledge level: curated
agent type: not_provided
- id: infores:bgee
status: released
name: Bgee
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Bgee
synonym:
- BGEE
knowledge level: curated
agent type: not_provided
- id: infores:bigclam
status: deprecated
name: Big Cell Line Association Miner
xref:
- https://github.com/PriceLab/translator-bigquery-api
synonym:
- BigClam
knowledge level: correlation
agent type: not_provided
- id: infores:bigg-models
status: released
name: BiGG Models
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BiGG-Models
synonym:
- BIGG
knowledge level: curated
agent type: not_provided
description: a knowledgebase of genome-scale metabolic network reconstructions
- id: infores:biggim
status: deprecated
name: Big Gene Interaction Miner
xref:
- https://github.com/PriceLab/translator-bigquery-api/
synonym:
- BigGIM
knowledge level: correlation
agent type: not_provided
- id: infores:bindingdb
status: released
name: BindingDB
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/bindingdb
synonym:
- The Binding Database
knowledge level: curated
agent type: not_provided
description: >-
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.
- id: infores:bio2rdf
status: released
name: Bio2RDF
xref:
- https://bio2rdf.org
knowledge level: curated
agent type: not_provided
- id: infores:biocatalogue
status: deprecated
name: BioCatalogue
- id: infores:biogrid
status: released
name: 'The Biological General Repository for Interaction Datasets '
xref:
- https://thebiogrid.org/
synonym:
- BioGrid
knowledge level: curated
agent type: not_provided
- id: infores:biolink-api
status: released
name: BioLink API
xref:
- https://api.monarchinitiative.org/api/
knowledge level: curated
agent type: not_provided
description: API integration layer for linked biological objects.
- id: infores:biolink-model-lookup
status: released
name: Biolink Model Lookup
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Biolink-Lookup-Service
knowledge level: curated
agent type: not_provided
description: Biolink Model Lookup service.
- id: infores:biolink-ontology
status: released
name: Biolink ontology
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioLink-OWL
knowledge level: curated
agent type: not_provided
- id: infores:bioportal
status: released
name: National Center for Biomedical Ontology BioPortal
xref:
- http://bioportal.bioontology.org/
synonym:
- bioportal
knowledge level: curated
agent type: not_provided
- id: infores:biothings-biggim-1
status: deprecated
name: Big GIM 1 API
knowledge level: curated
agent type: not_provided
description: Documentation of the Big GIM 1 KP query web services.
- id: infores:biothings-dgidb
status: released
name: BioThings DGIdb API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-DGIdb-API
knowledge level: curated
agent type: not_provided
description: Documentation of the BioThings DGIdb query web services.
- id: infores:biothings-diseases
status: released
name: BioThings DISEASES API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-DISEASES-API
knowledge level: curated
agent type: not_provided
description: Documentation of the DISEASES query web services.
- id: infores:biothings-ebi-gene2phenotype
status: released
name: BioThings EBIgene2phenotype API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-EBI-Gene2Phenotype
knowledge level: curated
agent type: not_provided
description: Documentation of the EBIgene2phenotype query web services.
- id: infores:biothings-explorer
status: released
name: BioThings Explorer
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-Explorer-(BTE)
synonym:
- BTE
knowledge level: curated
agent type: not_provided
- id: infores:service-provider-trapi
status: released
name: Service Provider TRAPI endpoints
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Service-Provider-TRAPI
synonym:
- service provider
knowledge level: curated
agent type: not_provided
- id: infores:biothings-go-bp
status: released
name: BioThings Gene Ontology Biological Process API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-GO-BP
knowledge level: curated
agent type: not_provided
description: Documentation of the Gene Ontology Biological Process query web services.
- id: infores:biothings-go-cc
status: released
name: BioThings Gene Ontology Cellular Component API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-GO-CC
knowledge level: curated
agent type: not_provided
description: Documentation of the Gene Ontology Cellular Component query web services.
- id: infores:biothings-go-mf
status: released
name: BioThings Gene Ontology Molecular Activity API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-GO-MF
knowledge level: curated
agent type: not_provided
description: Documentation of the Gene Ontology Molecular Activity query web services.
- id: infores:biothings-hpo
status: released
name: BioThings Human Phenotype Ontology API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-HPO
knowledge level: curated
agent type: not_provided
description: Documentation of the HPO query web services.
- id: infores:biothings-idisk
status: released
name: BioThings iDISK API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-IDISK
knowledge level: curated
agent type: not_provided
- id: infores:biothings-mgi-g2p
status: released
name: BioThings MGIgene2phenotype API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-MGI-G2P
knowledge level: curated
agent type: not_provided
description: Documentation of the MGIgene2phenotype query web services.
- id: infores:biothings-multiomics-biggim-drugresponse
status: released
name: Multiomics BigGIM-DrugResponse KP API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Big-GIM-II:-Drug-Response-KP
- https://github.com/NCATS-Tangerine/BigGIM_APIWrapper
knowledge level: curated
agent type: not_provided
description: Documentation of the Drug Response KP query web services.
- id: infores:biothings-multiomics-ehr-risk
status: modified
name: Multiomics EHR Risk KP API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP
knowledge level: correlation
agent type: not_provided
description: >-
Documentation of the Multiomics Electronic-Health-Record (EHR) Risk
KP query web services.
- id: infores:providence-st-joseph-ehr
status: released
name: Providence St. Joseph EHR Data
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Data
knowledge level: curated
agent type: not_provided
description: >-
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 [email protected] for more information.
- id: infores:biothings-multiomics-wellness
status: released
name: Multiomics Wellness KP API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Wellness-KP
knowledge level: correlation
agent type: not_provided
description: Documentation of the Multiomics Wellness KP query web services.
- id: infores:biothings-multiomics-clinicaltrials
status: released
name: Multiomics ClinicalTrials KP API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP
knowledge level: curated
agent type: not_provided
- id: infores:biothings-pfocr
status: modified
name: BioThings PFOCR API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-PFOCR
knowledge level: predicted
agent type: not_provided
description: Documentation of the pfocr query web services.
- id: infores:pfocr
status: released
name: PFOCR
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/pfocr
knowledge level: predicted
agent type: not_provided
- id: infores:biothings-semmeddb
status: released
name: BioThings SEMMEDDB API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-SEMMED-DB
knowledge level: text_mined
agent type: not_provided
description: Documentation of the BioThings SEMMEDDB query web services.
- id: infores:biothings-semmeddb-anatomy
status: deprecated
name: SEMMED Anatomy API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-SEMMED-DB-Anatomy
knowledge level: text_mined
agent type: not_provided
description: >-
Documentation of the SEMMED disease query web services. Learn more
about [mydisease.info](http://pending.biothings.io/semmed)
- id: infores:biothings-semmeddb-biological-process
status: deprecated
name: SEMMED Biological Process API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-SEMMED-DB-Biological-Process
knowledge level: text_mined
agent type: not_provided
description: >-
Documentation of the SEMMED disease query web services. Learn more
about [mydisease.info](http://pending.biothings.io/semmed)
- id: infores:biothings-semmeddb-chemical
status: deprecated
name: SEMMED Chemical API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-SEMMED-DB-Chemical
knowledge level: text_mined
agent type: not_provided
description: >-
Documentation of the SEMMED disease query web services. Learn more
about [mydisease.info](http://pending.biothings.io/semmed)
- id: infores:biothings-semmeddb-disease
status: deprecated
name: SEMMED Disease API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-SEMMED-DB-Disease
knowledge level: text_mined
agent type: not_provided
description: >-
Documentation of the SEMMED disease query web services. Learn more
about [semmed disease](http://pending.biothings.io/semmed)
- id: infores:biothings-semmeddb-gene
status: deprecated
name: SEMMED Gene API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-SEMMED-DB-Gene
knowledge level: text_mined
agent type: not_provided
description: Documentation of the SEMMED disease query web services. Learn more
about [mydisease.info](http://pending.biothings.io/semmed)
- id: infores:biothings-semmeddb-phenotype
status: deprecated
name: SEMMED Phenotype API
xref:
- https://github.com/biothings
knowledge level: text_mined
agent type: not_provided
description: Documentation of the SEMMED disease query web services. Learn more
about [mydisease.info](http://pending.biothings.io/semmed)
- id: infores:biothings-tcga-mut-freq
status: deprecated
name: Multiomics TCGA Mutation Frequency KP API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-CAM-AOP
knowledge level: correlation
agent type: not_provided
description: Documentation of the TCGA Mutation Frequency KP query web services.
- id: infores:biothings-uberon-ontology
status: released
name: BioThings UBERON Ontology API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-UBERON-Ontology
knowledge level: curated
agent type: not_provided
description: Documentation of the UBERON query web services.
- id: infores:biothings-rhea
status: released
name: BioThings Rhea API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-RHEA-API
knowledge level: curated
agent type: not_provided
description: Documentation of the BioThings Rhea query web services.
- id: infores:rhea
status: released
name: Rhea
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/rhea
knowledge level: curated
agent type: not_provided
description: https://www.rhea-db.org/
- id: infores:biothings-bioplanet-pathway-disease
status: released
name: BioThings BioPlanet Pathway-Disease API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-bioplanet-pathway-disease
knowledge level: curated
agent type: not_provided
description: >-
Documentation of the BioThings [BioPlanet](https://tripod.nih.gov/bioplanet/#)
pathway-disease association query web services.
- id: infores:biothings-bioplanet-pathway-gene
status: released
name: BioThings BioPlanet Pathway-Gene API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-bioplanet-pathway-gene
knowledge level: curated
agent type: not_provided
description: >-
Documentation of the BioThings [BioPlanet](https://tripod.nih.gov/bioplanet/#)
pathway-gene association query web services.
- id: infores:bioplanet
status: released
name: BioPlanet
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/bioplanet
knowledge level: curated
agent type: not_provided
description: https://tripod.nih.gov/bioplanet/#
- id: infores:biothings-bindingdb
status: released
name: BioThings BindingDB API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/BioThings-Binding-DB
knowledge level: curated
agent type: not_provided
description: >-
Documentation of the BioThings [BindingDB](https://www.bindingdb.org/rwd/bind/index.jsp)
query web services.
- id: infores:bspo
status: released
name: Biological Spatial Ontology
xref:
- https://obofoundry.org/ontology/bspo.html
synonym:
- BSPO
knowledge level: curated
agent type: not_provided
- id: infores:wbbt
status: released
name: C. elegans Gross Anatomy Ontology
xref:
- https://obofoundry.org/ontology/wbbt.html
synonym:
- WBBT
knowledge level: curated
agent type: not_provided
description: A structured controlled vocabulary of the anatomy of Caenorhabditis elegans.
- id: infores:wbphenotype
status: released
name: C. elegans phenotype
xref:
- https://obofoundry.org/ontology/wbphenotype.html
synonym:
- WBPhenotype
knowledge level: curated
agent type: not_provided
description: A structured controlled vocabulary of Caenorhabditis elegans phenotypes
- id: infores:cam-kp
status: deprecated
name: CAM-KP API
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-CAM-AOP
synonym:
- Causal Activity Model KP
knowledge level: curated
agent type: not_provided
description: TRAPI interface to database of Causal Activity Models
- id: infores:campfhir
status: deprecated
name: Clinical Asset Mapping Program for FHIR
xref:
- https://researchsoftwareinstitute.github.io/data-translator/apps/camp-fhir
synonym:
- CAMP FHIR
knowledge level: curated
agent type: not_provided
- id: infores:chebi
status: released
name: Chemical Entity of Biological Interest
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/ChEBI
synonym:
- ChEBI
knowledge level: curated
agent type: not_provided
description: a freely available dictionary of molecular entities focused on ‘small’ chemical compounds
- id: infores:chem2bio2rdf
status: released
name: Chem2bio2RDF
xref:
- http://cheminfov.informatics.indiana.edu:8080/c2b2r/
knowledge level: curated
agent type: not_provided
- id: infores:chembank
status: released
name: ChemBank
knowledge level: curated
agent type: not_provided
description: Initiative for Chemical Genetics contract from the National Cancer Institute
- id: infores:chembio
status: deprecated
name: ChemBio
knowledge level: curated
agent type: not_provided
- id: infores:chembl
status: released
name: ChEMBL
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/ChEMBL
synonym:
- Chembl
knowledge level: curated
agent type: not_provided
description: a manually curated database of bioactive molecules with drug-like properties.
- id: infores:chemotext
status: deprecated
name: Chemotext
xref:
- http://chemotext.mml.unc.edu/
knowledge level: curated
agent type: not_provided
- id: infores:civic
status: released
name: Clinital Interpretation of Variants in Cancer
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/civic
synonym:
- CIViC
knowledge level: curated
agent type: not_provided
- id: infores:cl
status: released
name: Cell Ontology
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/CL
synonym:
- CL
knowledge level: curated
agent type: not_provided
- id: infores:clingen
status: released
name: Clinical Genome Resource (ClinGen)
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/clingen
knowledge level: curated
agent type: not_provided
description: >-
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
- id: infores:clinical-profiles
status: deprecated
name: Clinical Profiles
knowledge level: curated
agent type: not_provided
- id: infores:clinicaltrials
status: released
name: ClinicalTrials.gov
xref:
- https://clinicaltrials.gov
knowledge level: curated
agent type: not_provided
- id: infores:clinvar
status: released
name: ClinVar
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/clinvar
knowledge level: curated
agent type: not_provided
description: >-
ClinVar is a freely accessible, public archive of reports of the
relationships among human variations and phenotypes, with supporting evidence.
- id: infores:cmap
status: released
name: Connectivity Map
xref:
- https://clue.io/cmap
synonym:
- CMAP
knowledge level: curated
agent type: not_provided
description: >-
genome-scale library of cellular signatures that catalogs transcriptional
responses to chemical, genetic, and disease perturbation"'
- id: infores:columbia-cdw-ehr-data
status: released
name: Columbia Clinical Data Warehouse for Health Patient EHR Data
xref:
- https://www.irvinginstitute.columbia.edu/services/clinical-data-warehouse-cdw-navigator-support
synonym:
- 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.
knowledge level: curated
agent type: not_provided
- id: infores:cohd
status: released
name: Columbia Open Health Data (COHD)
xref:
- https://github.com/NCATSTranslator/Translator-All/wiki/COHD-KP
knowledge level: correlation
agent type: not_provided
description: >-
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