The vast and complex materials design space demands innovative strategies to integrate multidisciplinary scientific knowledge and optimize materials discovery. While large language models (LLMs) have demonstrated promising reasoning and automation capabilities across various domains, their application in materials science remains limited due to a lack of benchmarking standards and practical implementation frameworks. To address these challenges, we introduce Mixture-of-Workflows for Self-Corrective Retrieval-Augmented Generation (CRAG-MoW) - a novel paradigm that orchestrates multiple agentic workflows employing distinct CRAG strategies using open-source LLMs. Unlike prior approaches, CRAG-MoW synthesizes diverse outputs through an orchestration agent, enabling direct evaluation of multiple LLMs across the same problem domain. We benchmark CRAG-MoWs across small molecules, polymers, and chemical reactions, as well as multi-modal nuclear magnetic resonance (NMR) spectral retrieval. Our results demonstrate that CRAG-MoWs achieve performance comparable to GPT-4o while being preferred more frequently in comparative evaluations, highlighting the advantage of structured retrieval and multi-agent synthesis. By revealing performance variations across data types, CRAG-MoW provides a scalable, interpretable, and benchmark-driven approach to optimizing AI architectures for materials discovery. These insights are pivotal in addressing fundamental gaps in benchmarking LLMs and autonomous AI agents for scientific applications.

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are continuously produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph encompassing biological knowledge about RNAs gathered from more than 50 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to automatically construct them. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluate the ecosystem by surveying open-source KG construction methods and analyzing its computational performance when constructing 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

Graph Representation Learning (GRL) methods opened new avenues for addressing complex, real-world problems represented by graphs. However, many graphs used in these applications comprise millions of nodes and billions of edges and are beyond the capabilities of current methods and software implementations. We present GRAPE, a software resource for graph processing and embedding that can scale with big graphs by using specialized and smart data structures, algorithms, and a fast parallel implementation of random walk-based methods. Compared with state-of-the-art software resources, GRAPE shows an improvement of orders of magnitude in empirical space and time complexity, as well as a competitive edge and node label prediction performance. GRAPE comprises about 1.7 million well-documented lines of Python and Rust code and provides 69 node embedding methods, 25 inference models, a collection of efficient graph processing utilities and over 80,000 graphs from the literature and other sources. Standardized interfaces allow seamless integration of third-party libraries, while ready-to-use and modular pipelines permit an easy-to-use evaluation of GRL methods, therefore also positioning GRAPE as a software resource to perform a fair comparison between methods and libraries for graph processing and embedding.

Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. Objective: We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Results: Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. Conclusions: By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.

Pharmacokinetic natural product-drug interactions (NPDIs) occur when botanical natural products are co-consumed with pharmaceutical drugs. Understanding mechanisms of NPDIs is key to preventing adverse events. We constructed a knowledge graph framework, NP-KG, as a step toward computational discovery of pharmacokinetic NPDIs. NP-KG is a heterogeneous KG with biomedical ontologies, linked data, and full texts of the scientific literature, constructed with the Phenotype Knowledge Translator framework and the semantic relation extraction systems, SemRep and Integrated Network and Dynamic Reasoning Assembler. NP-KG was evaluated with case studies of pharmacokinetic green tea- and kratom-drug interactions through path searches and meta-path discovery to determine congruent and contradictory information compared to ground truth data. The fully integrated NP-KG consisted of 745,512 nodes and 7,249,576 edges. Evaluation of NP-KG resulted in congruent (38.98% for green tea, 50% for kratom), contradictory (15.25% for green tea, 21.43% for kratom), and both congruent and contradictory (15.25% for green tea, 21.43% for kratom) information. Potential pharmacokinetic mechanisms for several purported NPDIs, including the green tea-raloxifene, green tea-nadolol, kratom-midazolam, kratom-quetiapine, and kratom-venlafaxine interactions were congruent with the published literature. NP-KG is the first KG to integrate biomedical ontologies with full texts of the scientific literature focused on natural products. We demonstrate the application of NP-KG to identify pharmacokinetic interactions involving enzymes, transporters, and pharmaceutical drugs. We envision that NP-KG will facilitate improved human-machine collaboration to guide researchers in future studies of pharmacokinetic NPDIs. The NP-KG framework is publicly available at https://doi.org/10.5281/zenodo.6814507 and https://github.com/sanyabt/np-kg.

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.