35 skills found · Page 1 of 2
althonos / ProntoA Python frontend to (Open Biomedical) Ontologies.
obi-ontology / ObiThe Ontology for Biomedical Investigations
callahantiff / OMOP2OBOOMOP2OBO: A Python Library for mapping OMOP standardized clinical terminologies to Open Biomedical Ontologies
biopragmatics / Pyobo📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures
iqvianlp / OntologyRAGOntologyRAG: Better and Faster Biomedical Code Mapping with Retrieval-Augmented Generation (RAG) Leveraging Ontology Knowledge Graph and In-context-learning (ICL) in Large Language Models
jamesaoverton / Obo TutorialA tutorial on using Open Biological and Biomedical Ontologies (OBO)
rcolinp / Clinical Informatics UmlsAn exploratory, tutorial and analytical view of the Unified Medical Language System (UMLS) & the software/technologies provided via being a free UMLS license holder. This repo will subset 2021AB UMLS native release, introduce/build upon UMLS provided tools to load a configured subset into first a relational database --> MySQL, SQLite, PostgreSQL and MariaDB all covered within this repo. Next the UMLS subset which is stored in a relational DB will be queried, modeled and lastly loaded into a defined Neo4j label property graph. Lastly, Neo4j database containing UMLS 2021AB subset in schema promoting intuitive analysis and rich visualization will become the central datastore for analysis. The datastore contains ~5 million distinct nodes & >40 million distinct relationships (edges). Currently, Neo4j is running via Docker but deployment options are NOT limited to Docker. If choosing to deploy via Neo4j Aura, server, Neo4j Desktop, VM etc... Please note and be aware of the specific volumes and environment variables specified within this repository (docker run). The ability for the loaded Neo4j Graph to interact with RDF data (i.e. import/export RDF data to and from Neo4j) may not be possible via all Neo4j deployment avenues (i.e. Neo4j Aura currently does not support RDF integration that is demonstrated in this repository).
OBOFoundry / COBAn experimental ontology containing key terms from Open Biological and Biomedical Ontologies (OBO)
fastobo / Fastobo PyFaultless AST for Open Biomedical Ontologies in Python.
fastobo / FastoboFaultless AST for Open Biomedical Ontologies.
lasigeBioTM / BiOntBiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction
OBOFoundry / OBO DashboardSummary Dashboard for Open Biological and Biomedical Ontologies
cidgoh / LexMaprLexMapr: A Lexicon and Rule-Based Tool for Translating Short Biomedical Specimen Descriptions into Semantic Web Ontology Terms
julianmendez / CelA lightweight Description Logic reasoner for large-scale biomedical ontologies
SotirisKot / Content Aware Node2VecSource code and Datasets of "Embedding Biomedical Ontologies by Jointly Encoding Network Structure and Textual Node Descriptors"
lasigeBioTM / BOLSTMClassifying Relations via Long Short-Term Memory Networks along Biomedical Ontologies
lias-laboratory / BiogitomBioGITOM: Matching Biomedical Ontologies with Graph Isomorphism Transformer
PROconsortium / PRoteinOntologyNo description available
OussamaBouaggad / Quantization[Frontiers'25] Search-Optimized Quantization in Biomedical Ontology Alignment
rubalsxngh / MedGraph Biomedical Knowledge Graph With Mondo OntologyMedGraph is a project focused to construct biomedical knowledge graph. It harnesses the power of pubMed for data retrieval, spaCy for NLP, Mondo Ontology for semantic enrichment, and pywikibot for integrating external knowledge. The final step involves deploying the graph onto the Neo4j database, creating a platform to explore medical information.
