GitHub topics: ncats-translator
NCATS-Tangerine/translator-api-registry
This repo hosts the API metadata for the Translator project
Language: Jupyter Notebook - Size: 8.51 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 13 - Forks: 31
biothings/biothings_explorer
TRAPI service for BioThings Explorer
Language: Vue - Size: 10.7 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 10 - Forks: 11
RTXteam/RTX
Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)
Language: Python - Size: 210 MB - Last synced at: about 7 hours ago - Pushed at: about 9 hours ago - Stars: 34 - Forks: 22
TranslatorSRI/NameResolution
A service for finding CURIEs from lexical strings.
Language: Python - Size: 352 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 2
TranslatorSRI/NodeNormalization
Service that produces Translator compliant nodes given a curie
Language: Python - Size: 610 KB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 10 - Forks: 6
ExposuresProvider/cam-pipeline
Data loading pipeline for CAM database
Language: Jupyter Notebook - Size: 51.3 MB - Last synced at: 1 day ago - Pushed at: 6 days ago - Stars: 2 - Forks: 4
biolink/biolink-model-toolkit
A collection of useful python functions for looking up information and working with the Biolink Model
Language: Python - Size: 6.76 MB - Last synced at: 4 days ago - Pushed at: about 2 months ago - Stars: 24 - Forks: 11
TranslatorSRI/Babel
Babel creates cliques of equivalent identifiers across many biomedical vocabularies.
Language: Python - Size: 9.83 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 9 - Forks: 2
biothings/myvariant.info
MyVariant.info: A BioThings API for human variant annotations
Language: Python - Size: 12.9 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 93 - Forks: 32
NCATSTranslator/Relay
Autonomous relay system for NCATS Biomedical Data Translator
Language: Python - Size: 2.55 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 5 - Forks: 25
RTXteam/RTX-KG2
Build system for the RTX-KG2pre biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
Language: Python - Size: 4.22 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 39 - Forks: 8
biolink/kgx
KGX is a Python library for exchanging Knowledge Graphs
Language: Python - Size: 7.41 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 123 - Forks: 29
SkyeAv/Tablassert
Tablassert is a multipurpose tool that crafts knowledge assertions from tabular data, augments knowledge with configuration, and exports knowledge as Knowledge Graph Exchange (KGX) consistent TSVs.
Language: Python - Size: 98.6 KB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 1 - Forks: 0
Translator-CATRAX/MULTIOMICS_KG
Here are the configs for MultiomicsKG. Feel free to add or edit any of these as you see fit. There's a config checker and guidelines here too.
Language: Python - Size: 3.02 MB - Last synced at: 10 days ago - Pushed at: 19 days ago - Stars: 1 - Forks: 0
biolink/biolink-model
Schema and generated objects for biolink data model and upper ontology
Language: Python - Size: 306 MB - Last synced at: 12 days ago - Pushed at: 19 days ago - Stars: 192 - Forks: 76
Translator-CATRAX/curie-clean
A Clojure utility for analyzing and resolving duplicate nodes in knowledge graph exchange (KGX) formatted knowledge graphs, with Tablassert integration and Biolink Model compliance. It rewrites Tablassert-integrated "table_configs" through a CLI.
Language: Clojure - Size: 50.8 KB - Last synced at: 21 days ago - Pushed at: 21 days ago - Stars: 1 - Forks: 0
biothings/mygene.info
MyGene.info: A BioThings API for gene annotations
Language: Python - Size: 2.87 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 124 - Forks: 20
SmartAPI/smartAPI
Intelligent APIs for a more connected web: https://smart-api.info
Language: Vue - Size: 41 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 22 - Forks: 18
webyrd/mediKanren
Proof-of-concept for reasoning over the SemMedDB knowledge base, using miniKanren + heuristics + indexing.
Language: Racket - Size: 28.1 MB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 328 - Forks: 53
SuLab/DrugMechDB
A database of paths that represent the mechanism of action from a drug to a disease in an indication.
Language: Jupyter Notebook - Size: 1.65 GB - Last synced at: 16 days ago - Pushed at: over 1 year ago - Stars: 59 - Forks: 18
INCATools/ubergraph
Integrated OBO ontology store
Language: Makefile - Size: 169 KB - Last synced at: about 2 months ago - Pushed at: 2 months ago - Stars: 44 - Forks: 3
NCATSTranslator/TranslatorTechnicalDocumentation
Official Developer Documentation repository for the Biomedical Data Translator
Size: 620 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 17
namin/biohacker
debugging biological networks to reach coherence, completeness and consistency
Language: Common Lisp - Size: 6.26 MB - Last synced at: 5 days ago - Pushed at: about 1 year ago - Stars: 46 - Forks: 8
suihuanglab/improving-agent
An Autonomous Reasoning Agent in the NCATS Biomedical Translator Network that uses EHR and multi-omic cohorts to rank results from user queries
Language: Python - Size: 796 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 4
TranslatorSRI/reasoner-pydantic
Pydantic models for the Reasoner API data formats
Language: Python - Size: 194 KB - Last synced at: 9 days ago - Pushed at: 5 months ago - Stars: 4 - Forks: 0
ranking-agent/aragorn
A Translator ARA combining asynchronous database querying, answer coalescence, and answer ranking.
Language: Python - Size: 4.15 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 4 - Forks: 3
ranking-agent/strider
A TRAPI-compliant component of ARAGORN that queries distributed KPs and assembles answers to user questions.
Language: Python - Size: 2.96 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0
biothings/smartapi-kg.js
A nodejs library for generate knowledge graphs based on SmartAPI Specifications
Language: TypeScript - Size: 3.32 MB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 4
ranking-agent/kp-registry
Knowledge Provider Registry
Language: Python - Size: 74.2 KB - Last synced at: 8 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
biothings/biothings.api
BioThings API framework - Making high-performance API for biological annotation data
Language: Python - Size: 30.8 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 46 - Forks: 26
biothings/bte_trapi_query_graph_handler
Module to handle TRAPI query and return TRAPI response
Language: TypeScript - Size: 5.25 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 6
biothings/call-apis.js
A nodejs module to make API calls for BioThings Explorer
Language: TypeScript - Size: 717 KB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 2 - Forks: 2
biothings/biomedical_id_resolver.js
js library for converting biological ids in batch
Language: TypeScript - Size: 931 KB - Last synced at: 3 days ago - Pushed at: 6 months ago - Stars: 1 - Forks: 2
ranking-agent/reasoner-transpiler
A library for converting TRAPI queries into cypher queries, taking into account the biolink predicate hierarchy
Language: Python - Size: 285 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 1
biothings/biolink-model.js
A nodejs library to consume biolink model
Language: TypeScript - Size: 580 KB - Last synced at: 3 days ago - Pushed at: 7 months ago - Stars: 0 - Forks: 2
ranking-agent/AnswerCoalesce
A TRAPI-compliant component of ARAGORN that groups together similar results.
Language: Python - Size: 105 MB - Last synced at: 7 months ago - Pushed at: 8 months ago - Stars: 2 - Forks: 0
biothings/api-respone-transform.js
A NodeJS library to transform API response into biolink model
Language: TypeScript - Size: 608 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 4
ranking-agent/gamma-viewer 📦
Language: JavaScript - Size: 4.78 MB - Last synced at: about 1 month ago - Pushed at: 8 months ago - Stars: 0 - Forks: 2
ranking-agent/QuestionRewrite 📦
A Swagger UI/web service interface for the Question Rewrite service
Language: Python - Size: 732 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
ranking-agent/aragorn-ranker
Exposes TRAPI functions to add literature co-occurrence edges, convert publications to edge weights, and provide scores for answers.
Language: Python - Size: 19.2 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 1
ExposuresProvider/icees-api
Language: Python - Size: 11.2 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 8
ranking-agent/robogallery
A collection of examples for the ranking-agent translator ecosystem
Language: Jupyter Notebook - Size: 5.21 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 1
TranslatorSRI/Plater
Plater automatically creates a TRAPI interface for a biolink-compliant neo4j graph.
Language: Python - Size: 587 KB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 1 - Forks: 7
biothings/mychem.info
MyChem.info: A BioThings API for chemical/drug annotations
Language: Python - Size: 23 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 15 - Forks: 12
ExposuresProvider/cam-kp-api 📦
Web service API for the NCATS Data Translator CAM-KP
Language: Scala - Size: 2.14 MB - Last synced at: 1 day ago - Pushed at: 12 months ago - Stars: 3 - Forks: 2
broadinstitute/depmap-api
API access for DepMap data
Language: Python - Size: 96.7 KB - Last synced at: 21 days ago - Pushed at: almost 6 years ago - Stars: 7 - Forks: 1
biothings/bte_schema_web_react
Language: JavaScript - Size: 19.4 MB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 2
NCATS-Tangerine/ndex-beacon
Knowledge Beacon wrapper for the NDex graph repository
Language: Java - Size: 435 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
NCATS-Tangerine/HMDB-knowledge-beacon
Knowledge beacon for the Human Metabolome Database
Language: Java - Size: 162 KB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
NCATS-Tangerine/beacon-aggregator Fork of STARInformatics/beacon-aggregator
A web service that operates over the Beacon network to provide a single software interface over the all the Beacons
Language: Java - Size: 3.78 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0
NCATS-Tangerine/beacon-validator
Simple application for testing validity of Knowledge Beacons
Language: Java - Size: 2.24 MB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
ExposuresProvider/FHIR-PIT
Language: Scala - Size: 160 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 1
ncats/translator-workflows
Language: Jupyter Notebook - Size: 67 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 12 - Forks: 6
NCATS-Tangerine/mvp-module-library
Collection of modules for executing MVP Workflows
Language: Jupyter Notebook - Size: 13.9 MB - Last synced at: 9 days ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 5
NCATS-Tangerine/tkbio
NCATS Translator Release 4.0 of Knowledge.Bio as a distributed knowledge map management platform
Language: Java - Size: 24.2 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 2
wikipathways/pathway-figure-ocr
Extracting gene sets from published pathway figures
Language: Jupyter Notebook - Size: 177 MB - Last synced at: 12 months ago - Pushed at: almost 2 years ago - Stars: 15 - Forks: 2
TomConlin/Transdipporator
prototype translator reasoner metadata for dipper rdf
Language: Awk - Size: 468 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 1
NCATS-Tangerine/translator-knowledge-beacon
NCATS Translator Knowledge Beacon Application Programming Interface plus Sample code
Language: Python - Size: 1.58 MB - Last synced at: 11 months ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 2
biothings/bte-trapi-workspace
A npm workspace setup for local development environment with all biothings explorer nodejs packages
Language: Shell - Size: 2.63 MB - Last synced at: over 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 5
biothings/biothings_explorer_jsonld 📦
Language: Python - Size: 110 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 4
biothings/biothings_explorer_web_old 📦
Web Interface for BioThings Explorer
Language: JavaScript - Size: 8.76 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 5 - Forks: 4
biothings/biothings_explorer_graphql
GraphQL app for BioThings Explorer
Language: JavaScript - Size: 782 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1
ExposuresProvider/iceesnn
Language: Python - Size: 4.88 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
NCATS-Infrared/gnbr-neo4j-database
Scripts for downloading, formatting, deploying GNBR neo4j instance
Language: Python - Size: 176 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 0
NCATS-Infrared/gnbr-server-python
Swagger server for GNBR knolwedge beacon api
Language: Python - Size: 30.3 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0
NCATS-Infrared/gnbr-client-python
Python client for GNBR KBAPI
Language: Python - Size: 122 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
NCATS-Infrared/iris-agent Fork of Ejhfast/iris-agent
A extensible conversational agent for data science tasks
Language: TeX - Size: 151 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
TomConlin/Semantic_Exchange_Format
Exploring what I need from a semantic graph fragment exchange format
Size: 30.3 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
TomConlin/bgee_coexpression
Translator CQ 1.6 redone with BGEE data
Language: Jupyter Notebook - Size: 3.73 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0
NCATS-Infrared/gnbr-beacon-api Fork of alavertu/GNBR_api
Global Network Derived from Text API system
Language: Python - Size: 7.62 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 0
TranslatorSRI/bl_lookup
Biolink Model Lookup Service
Language: Python - Size: 161 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
TranslatorSRI/ontology-kp
Translator Knowledge Provider for ontology triples
Language: Scala - Size: 301 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 2
biothings/biothings_explorer_archived 📦
BioThings Explorer: a schema-based client for API interoperability
Language: Jupyter Notebook - Size: 8.44 MB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 14
TranslatorSRI/BLComplianceService 📦
Validates a ReasonerAPI message for BioLink compliance
Language: Python - Size: 40 KB - Last synced at: about 1 month ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0
biothings/transform-api-response.js 📦
A nodejs library to transform API responses into biolink model
Size: 210 KB - Last synced at: about 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
realmarcin/MAK_results
Language: Python - Size: 1.27 GB - Last synced at: 18 days ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
biothings/biomedical-id-autocomplete.js
Language: JavaScript - Size: 10.3 MB - Last synced at: 9 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1
ExposuresProvider/icees-ui
Language: JavaScript - Size: 4.38 MB - Last synced at: almost 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
gglusman/data-fingerprints
Language: Python - Size: 95.7 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 7 - Forks: 3
NCATS-Tangerine/tranql
A Translator Query Language
Language: Python - Size: 4.92 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 6
TranslatorSRI/EdgeNormalization
A service for producing relationships compliant with the biolink model
Language: Python - Size: 58.6 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1
broadinstitute/sharpener-pathway-enrichment
Language: Java - Size: 177 KB - Last synced at: 10 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener
Gene-sharpener API
Language: Java - Size: 290 KB - Last synced at: 4 days ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 0
NCATSTranslator/TranslatorPM
Activities related to the overall project management for Translator
Size: 172 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 8
TranslatorSRI/reasoner-converter
Language: Python - Size: 42 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
NCATS-Tangerine/biolink-beacon
Monarch Biolink Knowledge Beacon implementation (as a Python Flask application)
Language: Python - Size: 34 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
biothings/biothings_resolver
A BioThings project for resolving identifiers among biological entities (aka "biothings")
Language: Python - Size: 163 KB - Last synced at: 5 days ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0
broadinstitute/sharpener-common-to-rare-disease-gene-producer
Common-to-rare disease gene-list producer
Language: Python - Size: 50.8 KB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
broadinstitute/reasoner
Reasoner
Language: Python - Size: 14.6 MB - Last synced at: 21 days ago - Pushed at: almost 5 years ago - Stars: 6 - Forks: 1
NCATSTranslator/KnowledgeProviderScaffold
Example Responses and Documentation for Knowledge Providers
Language: Python - Size: 45.9 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 2
broadinstitute/sharpener-gui
GUI for sharpener
Size: 60.6 MB - Last synced at: 4 days ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-depmap-expander
Gene-list expander based on DepMap gene-knockdown correlations
Language: Python - Size: 98.6 KB - Last synced at: 4 days ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-phenotype-similarity-expander
Phenotype similarity with shared HPO terms
Language: Python - Size: 101 KB - Last synced at: 10 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-random-producer
Language: Python - Size: 35.2 KB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-hypergeometric-enrichment-expander
Language: Python - Size: 43.9 KB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-hypergeometric-enrichment-filter
Language: Python - Size: 44.9 KB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-string-expander
Language: Python - Size: 43.9 KB - Last synced at: 2 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-disease-genes-producer
Gene-list producer based on disease-gene association
Language: Python - Size: 89.8 KB - Last synced at: 10 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-expression-correlation
BigGIM gene-expression correlation transformer for gene-list sharpener
Language: Python - Size: 61.5 KB - Last synced at: 4 days ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
broadinstitute/sharpener-bicluster-expander
RNAseqDB bi-cluster gene-to-gene links
Language: Python - Size: 40 KB - Last synced at: 10 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0