AIMC Topic: Knowledge Bases

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Toward a unified understanding of drug-drug interactions: mapping Japanese drug codes to RxNorm concepts.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVES: Linking information on Japanese pharmaceutical products to global knowledge bases (KBs) would enhance international collaborative research and yield valuable insights. However, public access to mappings of Japanese pharmaceutical products...

DRGKB: a knowledgebase of worldwide diagnosis-related groups' practices for comparison, evaluation and knowledge-guided application.

Database : the journal of biological databases and curation
As a prospective payment method, diagnosis-related groups (DRGs)'s implementation has varying effects on different regions and adopt different case classification systems. Our goal is to build a structured public online knowledgebase describing the w...

CyclicPepedia: a knowledge base of natural and synthetic cyclic peptides.

Briefings in bioinformatics
Cyclic peptides offer a range of notable advantages, including potent antibacterial properties, high binding affinity and specificity to target molecules, and minimal toxicity, making them highly promising candidates for drug development. However, a ...

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

Bioinformatics (Oxford, England)
MOTIVATION: Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and...

Extracting Drug-Protein Relation from Literature Using Ensembles of Biomedical Transformers.

Studies in health technology and informatics
Automatic extraction of relations between drugs/chemicals and proteins from ever-growing biomedical literature is required to build up-to-date knowledge bases in biomedicine. To promote the development of automated methods, BioCreative-VII organized ...

Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis.

Nucleic acids research
Plant Reactome (https://plantreactome.gramene.org) is a freely accessible, comprehensive plant pathway knowledgebase. It provides curated reference pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional speci...

The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem.

Nucleic acids research
In 2003, the Human Disease Ontology (DO, https://disease-ontology.org/) was established at Northwestern University. In the intervening 20 years, the DO has expanded to become a highly-utilized disease knowledge resource. Serving as the nomenclature a...

DrugBank 6.0: the DrugBank Knowledgebase for 2024.

Nucleic acids research
First released in 2006, DrugBank (https://go.drugbank.com) has grown to become the 'gold standard' knowledge resource for drug, drug-target and related pharmaceutical information. DrugBank is widely used across many diverse biomedical research and cl...

The Reactome Pathway Knowledgebase 2024.

Nucleic acids research
The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordere...

MACC: a visual interactive knowledgebase of metabolite-associated cell communications.

Nucleic acids research
Metabolite-associated cell communications play critical roles in maintaining the normal biological function of human through coordinating cells, organs and physiological systems. Though substantial information of MACCs has been continuously reported,...