Search Results - Database Programming Languages

Proceedings of the 19th International Symposium on Database Programming Languages

The 19th International Symposium on Database Programming Languages (DBPL)

Authors: Grust, Torsten

Pipeline to explore information on genome editing using large language models and genome editing meta-database.

Authors: Suzuki T Bono H

Source: Database : the journal of biological databases and curation [Database (Oxford)] 2025 Mar 08; Vol. 2025.

Publication Type: Journal Article

Journal Info: Publisher: Oxford Journals Country of Publication: England NLM ID: 101517697 Publication Model: Print Cited Medium: Internet ISSN: 1758-0463 (Electronic) Linking ISSN: 17580463 NLM ISO Abbreviation: Database (Oxford) Subsets: MEDLINE

MeSH Terms: Gene Editing* , Databases, Genetic* , Programming Languages*, Humans ; Animals ; Large Language Models

The 19th International Symposium on Database Programming Languages (DBPL)

Authors: Amir Shaikhha Torsten Grust

Source: Companion of the 2025 International Conference on Management of Data. :884-885

A case study using sewage metagenomic data for assessment of text-to-SQL capabilities in large language models.

Authors: Becsei Á Stéger J Visontai D et al.

Source: Scientific reports [Sci Rep] 2025 Nov 22; Vol. 15 (1), pp. 44557. Date of Electronic Publication: 2025 Nov 22.

Publication Type: Journal Article

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE

MeSH Terms: Sewage*/microbiology , Metagenomics*/methods , Programming Languages* , Metagenome*, Humans ; Databases, Factual ; Large Language Models

Verification and reproducible curation of the BioModels repository.

Authors: Smith LP Malik-Sheriff RS Nguyen TVN et al.

Source: PLoS computational biology [PLoS Comput Biol] 2025 Dec 04; Vol. 21 (12), pp. e1013239. Date of Electronic Publication: 2025 Dec 04 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101238922 Publication Model: eCollection Cited Medium: Internet ISSN: 1553-7358 (Electronic) Linking ISSN: 1553734X NLM ISO Abbreviation: PLoS Comput Biol Subsets: MEDLINE

MeSH Terms: Programming Languages* , Systems Biology*/methods , Data Curation*/methods , Databases, Factual* , Models, Biological*, Reproducibility of Results ; Computer Simulation ; Computational Biology/methods ; Humans

Biomedical Information Integration via Adaptive Large Language Model Construction.

Authors: Xue X Wu ME Khan F

Source: IEEE journal of biomedical and health informatics [IEEE J Biomed Health Inform] 2025 Sep; Vol. 29 (9), pp. 6381-6394.

Publication Type: Journal Article

Journal Info: Publisher: Institute of Electrical and Electronics Engineers Country of Publication: United States NLM ID: 101604520 Publication Model: Print Cited Medium: Internet ISSN: 2168-2208 (Electronic) Linking ISSN: 21682194 NLM ISO Abbreviation: IEEE J Biomed Health Inform Subsets: MEDLINE

MeSH Terms: Medical Informatics*/methods , Programming Languages*, Humans ; Algorithms ; Databases, Factual ; Large Language Models

Steering veridical large language model analyses by correcting and enriching generated database queries: first steps toward ChatGPT bioinformatics.

Authors: Cinquin O; Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California at Irvine, 4203 McGaugh Hall, Irvine, CA 92697, USA.

Source: Briefings in bioinformatics [Brief Bioinform] 2024 Nov 22; Vol. 26 (1).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Programming Languages* , Software* , Databases, Factual*, Genomics ; Humans ; Large Language Models ; Generative Artificial Intelligence

NutriGen: Personalized Meal Plan Generator Leveraging Large Language Models to Enhance Dietary and Nutritional Adherence.

Authors: Khamesian S Arefeen A Carpenter SM et al.

Source: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference [Annu Int Conf IEEE Eng Med Biol Soc] 2025 Jul; Vol. 2025, pp. 1-7.

Publication Type: Journal Article

Journal Info: Publisher: [IEEE] Country of Publication: United States NLM ID: 101763872 Publication Model: Print Cited Medium: Internet ISSN: 2694-0604 (Electronic) Linking ISSN: 23757477 NLM ISO Abbreviation: Annu Int Conf IEEE Eng Med Biol Soc Subsets: MEDLINE

MeSH Terms: Meals* , Diet* , Precision Medicine* , Language* , Programming Languages*, Humans ; Databases, Factual ; Large Language Models

Large Language Model-Based Critical Care Big Data Deployment and Extraction: Descriptive Analysis.

Authors: Yang Z Xu SS Liu X et al.

Source: JMIR medical informatics [JMIR Med Inform] 2025 Mar 12; Vol. 13, pp. e63216. Date of Electronic Publication: 2025 Mar 12.

Publication Type: Journal Article

Journal Info: Publisher: JMIR Publications Country of Publication: Canada NLM ID: 101645109 Publication Model: Electronic Cited Medium: Internet ISSN: 2291-9694 (Electronic) Linking ISSN: 22919694 NLM ISO Abbreviation: JMIR Med Inform Subsets: MEDLINE

MeSH Terms: Critical Care* , Big Data* , Programming Languages*, Humans ; Intensive Care Units ; Databases, Factual ; Large Language Models

Leveraging Large Language Models for Cancer Variant Classification: A Comparative Study of GPT-4o, LLaMA 3, and Qwen 2.5.

Authors: Lin KH Chen PC Kuo CT et al.

Source: Studies in health technology and informatics [Stud Health Technol Inform] 2025 Aug 07; Vol. 329, pp. 1728-1729.

Publication Type: Journal Article; Comparative Study

Journal Info: Publisher: IOS Press Country of Publication: Netherlands NLM ID: 9214582 Publication Model: Print Cited Medium: Internet ISSN: 1879-8365 (Electronic) Linking ISSN: 09269630 NLM ISO Abbreviation: Stud Health Technol Inform Subsets: MEDLINE

MeSH Terms: Neoplasms*/genetics , Neoplasms*/classification , Genetic Variation*/genetics , Natural Language Processing* , Programming Languages*, Humans ; Databases, Genetic ; Large Language Models

Facilitating analysis of open neurophysiology data on the DANDI Archive using large language model tools.

Authors: Magland JF Ly R Rübel O et al.

Source: Scientific data [Sci Data] 2025 Dec 16; Vol. 12 (1), pp. 1988. Date of Electronic Publication: 2025 Dec 16.

Publication Type: Journal Article; Dataset

Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101640192 Publication Model: Electronic Cited Medium: Internet ISSN: 2052-4463 (Electronic) Linking ISSN: 20524463 NLM ISO Abbreviation: Sci Data Subsets: MEDLINE

MeSH Terms: Neurophysiology* , Databases, Factual*, Humans ; Language ; Programming Languages ; Software ; Large Language Models

LitSumm: large language models for literature summarization of noncoding RNAs.

Authors: Green A Ribas CE Ontiveros-Palacios N et al.

Source: Database : the journal of biological databases and curation [Database (Oxford)] 2025 Feb 05; Vol. 2025.

Publication Type: Journal Article

Journal Info: Publisher: Oxford Journals Country of Publication: England NLM ID: 101517697 Publication Model: Print Cited Medium: Internet ISSN: 1758-0463 (Electronic) Linking ISSN: 17580463 NLM ISO Abbreviation: Database (Oxford) Subsets: MEDLINE

MeSH Terms: RNA, Untranslated*/genetics , Programming Languages* , Data Curation*/methods , Databases, Nucleic Acid*, Humans ; Software ; Large Language Models

Sharing Neuroimaging Data with Squirrel - A Relational Data Format to Store Raw to Analyzed Data and Everything in Between.

Authors: Book GA Calhoun VD Stevens MC et al.

Source: Neuroinformatics [Neuroinformatics] 2025 Jul 03; Vol. 23 (3), pp. 37. Date of Electronic Publication: 2025 Jul 03.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press, Inc Country of Publication: United States NLM ID: 101142069 Publication Model: Electronic Cited Medium: Internet ISSN: 1559-0089 (Electronic) Linking ISSN: 15392791 NLM ISO Abbreviation: Neuroinformatics Subsets: MEDLINE

MeSH Terms: Neuroimaging*/methods , Information Dissemination*/methods , Databases, Factual* , Software* , Information Storage and Retrieval*/methods , Programming Languages*, Humans ; Brain

Benchmarking large language models for identifying transcription factor regulatory interactions.

Authors: Noel L Hsiao YW He Y et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2026 Jan 02; Vol. 42 (1).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Transcription Factors*/metabolism , Transcription Factors*/genetics , Computational Biology*/methods , Gene Regulatory Networks* , Programming Languages*, Humans ; Benchmarking ; Large Language Models

Evaluation of large language models for discovery of gene set function.

Authors: Hu M Alkhairy S Lee I et al.

Source: Nature methods [Nat Methods] 2025 Jan; Vol. 22 (1), pp. 82-91. Date of Electronic Publication: 2024 Nov 28.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH Terms: Genomics*/methods , Computational Biology*/methods , Programming Languages*, Databases, Genetic ; Humans ; Gene Ontology ; Software ; Large Language Models

Pre-Meta: priors-augmented retrieval for LLM-based metadata generation.

Authors: Tinn P Sørbø S Jiang S et al.

Source: Bioinformatics (Oxford, England) [Bioinformatics] 2025 Oct 02; Vol. 41 (10).

Publication Type: Journal Article

Journal Info: Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE

MeSH Terms: Metadata* , Software* , Programming Languages* , Genomics*/methods , Information Storage and Retrieval*/methods , Computational Biology*/methods, Databases, Genetic ; High-Throughput Nucleotide Sequencing

Programming Languages and Systems

Contributors: Sergey, Ilya

Subject Terms: automata theory, computer programming, computer systems, databases, distributed computer systems, distributed systems, embedded systems, formal languages, formal logic, linguistics, ontologies, parallel processing systems, program compilers, programming languages, semantics, software design, software engineering, software quality, verification, Programming and scripting languages: general, Computer science, Algorithms and data structures, Network hardware, Computer programming / software engineering

File Description: application/pdf

Relation: Lecture Notes in Computer Science

Access URL: https://library.oapen.org/handle/20.500.12657/54028

AutoQUEST: A Chain-of-Thought Pipeline for Automated Question Generation and Validation in MAUDE Research.

Authors: Hua L Gong Y

Source: Studies in health technology and informatics [Stud Health Technol Inform] 2025 Aug 07; Vol. 329, pp. 421-425.

Publication Type: Journal Article

Journal Info: Publisher: IOS Press Country of Publication: Netherlands NLM ID: 9214582 Publication Model: Print Cited Medium: Internet ISSN: 1879-8365 (Electronic) Linking ISSN: 09269630 NLM ISO Abbreviation: Stud Health Technol Inform Subsets: MEDLINE

MeSH Terms: Databases, Factual* , Software* , Natural Language Processing* , Data Mining*/methods, Programming Languages ; Humans

Open-source large language models in action: A bioinformatics chatbot for PRIDE database.

Authors: Bai J Kamatchinathan S Kundu DJ et al.

Source: Proteomics [Proteomics] 2024 Nov; Vol. 24 (21-22), pp. e2400005. Date of Electronic Publication: 2024 Mar 31.

Publication Type: Journal Article

Journal Info: Publisher: Wiley-VCH Country of Publication: Germany NLM ID: 101092707 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1615-9861 (Electronic) Linking ISSN: 16159853 NLM ISO Abbreviation: Proteomics Subsets: MEDLINE

MeSH Terms: Computational Biology*/methods , Software* , Databases, Protein*, Proteomics/methods ; User-Computer Interface ; Programming Languages ; Internet ; Humans