TargetScanHumans 8.0
TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer, 7mer, & 6mer sites that match the seed region of each miRNA.
targetscan.org/vert_80/
github.com/biobricks-ai/targ…
github.com/biobricks-ai/targ…
Biobricks.ai transforms TargetScan into parquet files.
targetscan.org/cgi-bin/targe…
MirGeneDB 3.0
The curated microRNA Gene Database
MirGeneDB 3.0 (Clarke and Hoye et al. 2024 )
academic.oup.com/nar/article… includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA families from 114 metazoan species. All microRNAs can be browsed, searched & downloaded.
mirgenedb.org/
mirgenedb.org/information
miRBase
The microRNA database
The archive for microRNA sequences & annotations.
mirbase.org/
Scalable Precision Medicine Open Knowledge Engine (SPOKE)
spoke.ucsf.edu/home
SPOKE-RDF
An RDF version of the Scalable Precision Medicine Open Knowledge Engine (SPOKE), a biomedical Knowledge Graph (KG) connecting millions of concepts via semantically meaningful relationships.
github.com/biobricks-ai/spok…
📃 Biomedical knowledge graph-optimized prompt generation for large language models
Here, we introduce a token-optimized & robust Knowledge Graph-based Retrieval Augmented Generation (KG-RAG) framework by leveraging a massive biomedical KG (SPOKE) with LLMs such as Llama-2-13b, GPT-3.5-Turbo, and GPT-4, to generate meaningful biomedical text rooted in established knowledge.
academic.oup.com/bioinformat…
github.com/BaranziniLab/KG_R…
SPOKE Knowledge Graph (KG) Neighborhood
spoke.rbvi.ucsf.edu/neighbor…
SPOKE REST AI Swagger
spoke.rbvi.ucsf.edu/swagger/
Project Rephetio
Repurposing drugs on a hetnet
The hetnet was designed for Project Rephetio, which aims to systematically identify why drugs work & predict new therapies for drugs.
think-lab.github.io/p/rephet…
📃 Systematic integration of biomedical knowledge prioritizes drugs for repurposing
git.dhimmel.com/rephetio-man…
What is a "hetnet"?
A network (also known as a graph) is a conceptual representation of a group of things — called nodes — & the relationships between them — called edges. Typically, a network has only one type of node & one type of edge. But in many cases, it is necessary to be able to distinguish between different types of entities & relationships.
A hetnet (short for heterogeneous information network) is a network where nodes & edges can be multiple types. This additional dimension allows a hetnet to accurately describe more complex data. Hetnets are particularly useful in biomedicine, where it is important to capture the conceptual distinctions between various components & mechanisms, such as genes and diseases, or upregulation & binding.
het.io/about/#what-is-a-hetn…
Hetionet
Hetionet is an integrative network of biomedical knowledge assembled from 29 different databases of genes, compounds, diseases, and more. The network combines over 50 years of biomedical information into a single resource, consisting of 47,031 nodes (11 types) & 2,250,197 relationships (24 types).
het.io/
github.com/hetio/hetionet#li…
Hetionet in Neo4j
Neo4j is a database designed for hetnets (graphs w/ multiple node or relationship types). You’re currently interacting w/ Hetionet through the Neo4j Browser, which provides a web interface to the database. This is a read-only instance, so you can’t modify the network. However, you can run queries & explore the network.
neo4j.het.io/browser/
Hetnet Connectivity Search
het.io/search/
Hetnets in Python
github.com/hetio/hetnetpy
📃 Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
journals.plos.org/ploscompbi…
📃 Hetnet connectivity search provides rapid insights into how biomedical entities are related
academic.oup.com/gigascience…
📃 The probability of edge existence due to node degree: a baseline for network-based predictions
XSwap Edge Probability Baselines
academic.oup.com/gigascience…