SmartAPI/smartAPI

Intelligent APIs for a more connected web: https://smart-api.info

Language: Vue - Size: 41.5 MB - Last synced: about 17 hours ago - Pushed: about 17 hours ago - Stars: 20 - Forks: 16

biothings/mygene.info

MyGene.info: A BioThings API for gene annotations

Language: Python - Size: 2.83 MB - Last synced: about 15 hours ago - Pushed: about 19 hours ago - Stars: 110 - Forks: 20

webyrd/mediKanren

Proof-of-concept for reasoning over the SemMedDB knowledge base, using miniKanren + heuristics + indexing.

Language: Racket - Size: 28.3 MB - Last synced: about 18 hours ago - Pushed: about 19 hours ago - Stars: 316 - Forks: 53

biothings/smartapi-kg.js

A nodejs library for generate knowledge graphs based on SmartAPI Specifications

Language: TypeScript - Size: 3.37 MB - Last synced: about 22 hours ago - Pushed: 2 days ago - Stars: 0 - Forks: 4

biothings/bte_trapi_query_graph_handler

Module to handle TRAPI query and return TRAPI response

Language: TypeScript - Size: 4.99 MB - Last synced: about 22 hours ago - Pushed: 2 days ago - Stars: 0 - Forks: 6

biothings/biothings.api

BioThings API framework - Making high-performance API for biological annotation data

Language: Python - Size: 30.8 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 45 - Forks: 25

NCATS-Tangerine/translator-api-registry

This repo hosts the API metadata for the Translator project

Language: Jupyter Notebook - Size: 7.78 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 13 - Forks: 30

biothings/biothings_explorer

TRAPI service for BioThings Explorer

Language: Vue - Size: 9.5 MB - Last synced: about 22 hours ago - Pushed: 2 days ago - Stars: 8 - Forks: 9

TranslatorSRI/NodeNormalization

Service that produces Translator compliant nodes given a curie

Language: Python - Size: 430 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 9 - Forks: 6

NCATSTranslator/Relay

Autonomous relay system for NCATS Biomedical Data Translator

Language: Python - Size: 2.25 MB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 5 - Forks: 22

INCATools/ubergraph

Integrated OBO ontology store

Language: Makefile - Size: 193 KB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 41 - Forks: 3

biolink/biolink-model-toolkit

A collection of useful python functions for looking up information and working with the Biolink Model

Language: Python - Size: 6.57 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 20 - Forks: 10

ranking-agent/strider

A TRAPI-compliant component of ARAGORN that queries distributed KPs and assembles answers to user questions.

Language: Python - Size: 2.99 MB - Last synced: 7 days ago - Pushed: 9 days ago - Stars: 3 - Forks: 0

ranking-agent/aragorn

A Translator ARA combining asynchronous database querying, answer coalescence, and answer ranking.

Language: Python - Size: 3.91 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 4 - Forks: 3

biolink/biolink-model

Schema and generated objects for biolink data model and upper ontology

Language: Python - Size: 291 MB - Last synced: 16 days ago - Pushed: 17 days ago - Stars: 167 - Forks: 71

biothings/mychem.info

MyChem.info: A BioThings API for chemical/drug annotations

Language: Python - Size: 23 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 15 - Forks: 12

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: 764 KB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 2 - Forks: 4

RTXteam/RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)

Language: Python - Size: 4.17 MB - Last synced: 19 days ago - Pushed: 30 days ago - Stars: 32 - Forks: 7

ExposuresProvider/cam-pipeline

Data loading pipeline for CAM database

Language: Jupyter Notebook - Size: 51 MB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 2 - Forks: 4

TranslatorSRI/BLComplianceService 📦

Validates a ReasonerAPI message for BioLink compliance

Language: Python - Size: 40 KB - Last synced: 16 days ago - Pushed: about 3 years ago - Stars: 2 - Forks: 0

ranking-agent/AnswerCoalesce

A TRAPI-compliant component of ARAGORN that groups together similar results.

Language: Python - Size: 81.2 MB - Last synced: about 17 hours ago - Pushed: about 18 hours ago - Stars: 2 - Forks: 0

ExposuresProvider/icees-api

Language: Python - Size: 11.1 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 2 - Forks: 8

NCATSTranslator/TranslatorTechnicalDocumentation

Official Developer Documentation repository for the Biomedical Data Translator

Size: 524 KB - Last synced: 10 days ago - Pushed: 5 months ago - Stars: 3 - Forks: 12

RTXteam/RTX

Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)

Language: Python - Size: 209 MB - Last synced: 24 days ago - Pushed: 26 days ago - Stars: 34 - Forks: 20

TranslatorSRI/NameResolution

A service for finding CURIEs from lexical strings.

Language: Python - Size: 269 KB - Last synced: 23 days ago - Pushed: 23 days ago - Stars: 3 - Forks: 2

biothings/bte_schema_web_react

Language: JavaScript - Size: 19.4 MB - Last synced: 24 days ago - Pushed: 9 months ago - Stars: 0 - Forks: 2

biolink/kgx

KGX is a Python library for exchanging Knowledge Graphs

Language: Python - Size: 6.84 MB - Last synced: 15 days ago - Pushed: 17 days ago - Stars: 108 - Forks: 26

biothings/myvariant.info

MyVariant.info: A BioThings API for human variant annotations

Language: Python - Size: 12.9 MB - Last synced: 20 days ago - Pushed: 21 days ago - Stars: 85 - Forks: 32

TranslatorSRI/reasoner-pydantic

Pydantic models for the Reasoner API data formats

Language: Python - Size: 203 KB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 4 - Forks: 0

ranking-agent/reasoner-transpiler

A library for converting TRAPI queries into cypher queries, taking into account the biolink predicate hierarchy

Language: Python - Size: 236 KB - Last synced: 30 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

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: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

NCATS-Tangerine/ndex-beacon

Knowledge Beacon wrapper for the NDex graph repository

Language: Java - Size: 435 KB - Last synced: about 1 month ago - Pushed: over 4 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: about 1 month ago - Pushed: over 5 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: about 1 month ago - Pushed: over 3 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: about 1 month ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

TranslatorSRI/Babel

Babel creates cliques of equivalent identifiers across many biomedical vocabularies.

Language: Python - Size: 9.32 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 7 - Forks: 2

ExposuresProvider/FHIR-PIT

Language: Scala - Size: 160 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 1

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: about 1 month ago - Pushed: 8 months ago - Stars: 50 - Forks: 17

ncats/translator-workflows

Language: Jupyter Notebook - Size: 67 MB - Last synced: 20 days ago - Pushed: 20 days 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: 5 days ago - Pushed: over 4 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: about 1 month ago - Pushed: about 2 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: 14 days ago - Pushed: almost 1 year ago - Stars: 15 - Forks: 2

broadinstitute/sharpener-gui

GUI for sharpener

Size: 60.6 MB - Last synced: 3 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener-phenotype-similarity-expander

Phenotype similarity with shared HPO terms

Language: Python - Size: 101 KB - Last synced: 3 months ago - Pushed: 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: 3 months ago - Pushed: about 4 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: 3 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener

Gene-sharpener API

Language: Java - Size: 290 KB - Last synced: 3 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 0

broadinstitute/sharpener-bicluster-expander

RNAseqDB bi-cluster gene-to-gene links

Language: Python - Size: 40 KB - Last synced: 3 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener-pathway-enrichment

Language: Java - Size: 177 KB - Last synced: 3 months ago - Pushed: over 4 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: 3 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

TranslatorSRI/Plater

Plater automatically creates a TRAPI interface for a biolink-compliant neo4j graph.

Language: Python - Size: 499 KB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 1 - Forks: 7

namin/biohacker

debugging biological networks to reach coherence, completeness and consistency

Language: Common Lisp - Size: 6.26 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 41 - Forks: 8

biothings/call-apis.js

A nodejs module to make API calls for BioThings Explorer

Language: TypeScript - Size: 637 KB - Last synced: 10 days ago - Pushed: about 1 month ago - Stars: 2 - Forks: 2

TomConlin/Transdipporator

prototype translator reasoner metadata for dipper rdf

Language: Awk - Size: 468 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1

ExposuresProvider/cam-kp-api

Web service API for the NCATS Data Translator CAM-KP

Language: Scala - Size: 2.14 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 3 - Forks: 2

biothings/biomedical_id_resolver.js

js library for converting biological ids in batch

Language: TypeScript - Size: 914 KB - Last synced: 25 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 2

NCATS-Tangerine/translator-knowledge-beacon

NCATS Translator Knowledge Beacon Application Programming Interface plus Sample code

Language: Python - Size: 1.58 MB - Last synced: 16 days ago - Pushed: about 3 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: 9 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 5

biothings/biothings_explorer_jsonld 📦

Language: Python - Size: 110 KB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 4 - Forks: 4

biothings/biothings_explorer_web_old 📦

Web Interface for BioThings Explorer

Language: JavaScript - Size: 8.76 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 5 - Forks: 4

biothings/biothings_explorer_graphql

GraphQL app for BioThings Explorer

Language: JavaScript - Size: 782 KB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

ranking-agent/robogallery

A collection of examples for the ranking-agent translator ecosystem

Language: Jupyter Notebook - Size: 4.97 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 1

ExposuresProvider/iceesnn

Language: Python - Size: 4.88 KB - Last synced: 9 months ago - Pushed: about 4 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: 9 months ago - Pushed: over 4 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: 9 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

NCATS-Infrared/gnbr-client-python

Python client for GNBR KBAPI

Language: Python - Size: 122 KB - Last synced: 9 months ago - Pushed: over 5 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: 9 months ago - Pushed: almost 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: 10 months ago - Pushed: over 5 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: 10 months ago - Pushed: about 5 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: 9 months ago - Pushed: almost 6 years ago - Stars: 1 - Forks: 0

TranslatorSRI/bl_lookup

Biolink Model Lookup Service

Language: Python - Size: 161 KB - Last synced: almost 1 year ago - Pushed: almost 1 year ago - Stars: 0 - Forks: 0

TranslatorSRI/ontology-kp

Translator Knowledge Provider for ontology triples

Language: Scala - Size: 301 KB - Last synced: 11 months ago - Pushed: 11 months 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: 24 days ago - Pushed: almost 2 years ago - Stars: 14 - Forks: 14

broadinstitute/depmap-api

API access for DepMap data

Language: Python - Size: 96.7 KB - Last synced: 12 months ago - Pushed: almost 5 years ago - Stars: 6 - Forks: 2

realmarcin/MAK_results

Language: Python - Size: 1.27 GB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

biothings/api-respone-transform.js

A NodeJS library to transform API response into biolink model

Language: TypeScript - Size: 604 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 4

biothings/transform-api-response.js 📦

A nodejs library to transform API responses into biolink model

Size: 210 KB - Last synced: 27 days ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

biothings/biomedical-id-autocomplete.js

Language: JavaScript - Size: 10.3 MB - Last synced: 20 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 1

ExposuresProvider/icees-ui

Language: JavaScript - Size: 4.38 MB - Last synced: 11 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

gglusman/data-fingerprints

Language: Python - Size: 95.7 KB - Last synced: 12 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 3

biothings/biolink-model.js

A nodejs library to consume biolink model

Language: TypeScript - Size: 565 KB - Last synced: 11 days ago - Pushed: 2 months ago - Stars: 0 - Forks: 2

ranking-agent/kp-registry

Knowledge Provider Registry

Language: Python - Size: 72.3 KB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

NCATS-Tangerine/tranql

A Translator Query Language

Language: Python - Size: 4.92 MB - Last synced: about 1 month ago - Pushed: over 1 year 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: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

ranking-agent/gamma-viewer

Language: JavaScript - Size: 4.78 MB - Last synced: 14 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 2

NCATSTranslator/TranslatorPM

Activities related to the overall project management for Translator

Size: 172 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 8

TranslatorSRI/reasoner-converter

Language: Python - Size: 42 KB - Last synced: about 1 year ago - Pushed: over 3 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: about 1 month ago - Pushed: over 3 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: 9 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

ranking-agent/QuestionRewrite

A Swagger UI/web service interface for the Question Rewrite service

Language: Python - Size: 729 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - 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: 12 months ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

broadinstitute/reasoner

Reasoner

Language: Python - Size: 14.6 MB - Last synced: 12 months ago - Pushed: almost 4 years ago - Stars: 6 - Forks: 1

NCATSTranslator/KnowledgeProviderScaffold

Example Responses and Documentation for Knowledge Providers

Language: Python - Size: 45.9 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 2 - Forks: 2

broadinstitute/sharpener-random-producer

Language: Python - Size: 35.2 KB - Last synced: 12 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener-hypergeometric-enrichment-expander

Language: Python - Size: 43.9 KB - Last synced: 12 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener-hypergeometric-enrichment-filter

Language: Python - Size: 44.9 KB - Last synced: 12 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener-string-expander

Language: Python - Size: 43.9 KB - Last synced: 12 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener-remove-genes-filter

Language: Java - Size: 43 KB - Last synced: 12 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/sharpener-geneset-producer

producer of MSigDB gene sets for gene sharpener

Language: Java - Size: 51.8 KB - Last synced: 12 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

broadinstitute/gene_knockout_correlation

API access to gene knockout correlations based on Cancer Dependency Map (DepMap) data

Language: Java - Size: 18.6 KB - Last synced: 12 months ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0