links

to capture links to various resources

RDF interaction

• SPARQL Anything -- query local/remote documents with sparql, deploy local fuseki server with yasgui interface.
• YASGUI -- user interface for formulating SPARQL queries, with autocomplete.
• SPARKLIS -- interface that uses a controlled natural language to query SPARQL endpoints
• AtomGraph -- Linked Data Processor for SPARQL endpoints
• Sketch -- Compose/validate RDF and obtain a graphical visualization
• LodLive -- Explore SPARQL/IRI entities in a graphical manner.
• SPARQLNotebook -- SPARQL notebook for VSCode
• SPARQL-ML -- SPARQL microservices
• GRLC -- Expose SPARQL queries as serverless RESTful services
• SPARQL-Annotation-Syntax -- compatible with grlc services
• SANSA - SANSA is a big data engine for scalable processing of large-scale RDF data.
• OntoGen - RDF version control
• KinGVisher SPARQL endpoint graph visualization
• VoidGenerator
• SparqlEditor - yasgui with autocomplete
• Rudof - genenerate shex shapes and convert rdf
• Shexer - learn shex shapes from rdf files

RDF Graph Databases

• Virtuoso -- Virtuoso is a high-performance object-relational SQL database with WebDAV and SPARQL embedded into SQL for querying RDF data.
• GraphDB -- GraphDB is an enterprise ready Semantic Graph Database, compliant with W3C Standards.
• Blazegraph -- Blazegraph™ DB is a ultra high-performance graph database supporting Blueprints and RDF/SPARQL APIs.
• AllegroGraph -- AllegroGraph is a purpose built, horizontal sharding, high-performance, persistent, graph and document database
• Apache Jena TDB -- a native high performance triple store
• Apache Jena Fuseki
• Amazon Neptune -- hosted graph database
• RDFox -- in memory RDF triple store with reasoning
• OxiGraph -- Graph database based on RocksDb with SPARQL endpoint

RDF Validation

• SHACLOnlineValidator - online SHACL validator
• SoWasm - online RDF conversion tool
• EasyRDF Converter -- clean and transform RDF
• Turtle Validator
• YASHE -- A ShExeditor with syntax checking and autocomplete
• ShEx --
• ShEx forms -- Automatic form generation and ShEx validation tool by Eric P
• SHACL Playground -- validation tool for SHACL shapes
• SHACL Validator
• RDFShape -- to extract shapes from RDF graphs :: A Web app and library to extract SHACL/ShEx
• SheXer -- to extract shapes from RDF graphs :: A library for automatic extraction of SHACL/ShEx
• Shape Designer -- to extract shapes from RDF graphs :: A Java tool to extract SHACL/ShEx by Boneva et al
• Shapes induction method -- to extract shapes from RDF graphs :: RDF shape induction using knowledge base profiling to generate Shapes by Mihindukulasooriya et al.
• UnSHACLed -- to extract shapes from RDF graphs :: Defining constraints over RDF
• SHACLGEN -- to extract shapes from RDF graphs or Ontologies :: A Python library to extract SHACL shapes
• TopBraid Composer -- to extract shapes from RDF graphs or Ontologies
• TopBrain SHACL API
• Astrea -- to extract shapes from Ontologies :: Automatic extraction of SHACL shapes
• SHACL Play -- to extract shapes from Ontologies :: OWL to SHACL converter
• Shapes extraction using ontology patterns: -- to extract shapes from Ontologies :: Towards improving the quality of knowledge graphs with data-driven ontology patterns and SHACL by Spahiu et al.
• Protégé -- to define shapes manually
• Shaperone playground
• ShaclEditor

Ontology

• OntoFlow

Rule Learning & KG Embeddings

• AnyBURL
• PyClause
• SAFRAN
• AIME
• LibKGE
• PyKeen

Explainable AI

• Awesome Graph Explainability - graph explainability papers
• KELPIE - XAI framework for interpreting Link Predictions on Knowledge Graphs
• SHAP - SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any machine learning model.
• Pytorch Geometric - Pytorch GNN explainability

SPARQL Endpoints

• NeuroDKG
• FoodHealthClaims
• Bio2RDF
• Nanopubs
• GO
• UniProt
• DBPedia
• Wikidata -- GET only
• Wikipathways
• Riken
• RENCI-ubergraph
• KG-Hub
• LOD-by-OpenLink
• OMA - orthologous matrix
• Foodie-Cloud
• LSQ
• European Environment Agency
• LinkedLifeData
• EBI RDF - not functional (last checked 15-02-2023)
• SemOpenAlex

Knowledge Graphs

• PrimeKG
• DRKG
• HetIo
• Bioteque
• BioKG
• pyBioDataFuse
• PharmKG
• OpenBioLink
• Clinical Knowledge Graph
• RTX-KG2

Health Data

• UKBioBank
• FinnGen
• ADNI
• MIMIC
• YAIB - Yet Another ICU Benchmark (YAIB)

Drug Resources

• DrugCentral - curated drug indications
• DrugMechDB - curated drug mechanisms of action

Synthetic Data Generation

• DPCGANS -DP-CGANS (Differentially Private - Conditional Generative Adversarial NetworkS)
• OntoGAN - OntoGAN - conditioinal generation of tabular data using ontology embeddings.
• Syntho
• Synthetic Data Vault
• SynthEHR
• SyntheMol

Annotation

• Label Studio - Mixed annotation
• Prodigy - Annotation tool that uses active learning
• Hypothesis - Web page annotation
• Doccano - Text Annotation

Text Processing

• Readability measures
• SentenceBERT

Mapping

• Cocoda

Data Portal

• CKAN
• Omeka

Companies of Interest

• relationalAI
• stardog
• metaphacts
• ontoforce
• Graphable
• KatanaGraph
• TigerGraphDb - scalable graph database
• origintrail - decentralized knowledge graph

Policy

• Collibra ROI calculator
• PLOT4ai - Privacy Library Of Threats 4 Artificial Intelligence

Pipelines

• Orchest - visual python pipeline editor, executable over a kubernetes cluster

DeepLearning

• DiffSound - Text to Sound
• DALL-E2 - Text to Image
• GPT-4 - Text to Text
• CLIP- Contrastive Language-Image Pre-Training (CLIP)
• NExT-GPT - Any-to-Any Multi-modal GPT
• 4M - Apple's multi-modal language model
• StableDiffusion - A latent text-to-image diffusion model to generate photo-realistic images given any text input
• ExplainableAI - A list of xAI papers
• DGL -- Deep Graph Library is a Python package built for graph neural networks on top of existing DL frameworks (PyTorch, MXNet and TensorFlow)
• LangChain - Incorporates other elements with LLM
• CTransfomers - Python bindings for the Transformer models implemented in C/C++ using GGML library.
• GNNShap

Responsible AI

• MIDRC Bias awareness Tool
• MIDRC Diversity Calculator

Drug Discovery

• DeepPurpose
• Therapeutic Data Commons

LLM

• LangChain - Build context-aware, reasoning applications
• LlamaIndex - LLamaIndex framework for LLM applications
• LLMWare - LLM with RAG
• OLLama - Run Llama 2, Code Llama, and other models
• VLLM - LLM inference and serving
• LLAMACPP - python bindings for c++ implementation to access llama models
• privateGPT - API to build private, context-aware AI application
• blindChat - in-browser privacy solution to make Conversational AI privacy-friendly
• Text Splitter Playground
• LLAMA2
• BEHRT - EHR Transformer
• BLOOM - open source multi-modal, multi-lingual transfomer
• AwesomeGraphLLM - list of papers and code for graph llms
• TruLens - LLM evaluation
• GraphRAG - GraphRAG from microsoft
• CrewAI - CrewAI
• OpenR - open source LLM reasoning system