# Biomedical Text Mining and Ontologies

**Type:** Topics  
**Canonical URL:** https://scholariq.org/topics/biomedical-text-mining-and-ontologies/

## Facts

| Field | Value |
| --- | --- |
| Description | This cluster of papers focuses on the development and application of biomedical ontologies, text mining, and natural language processing techniques to extract and integrate knowledge from biomedical literature. It encompasses topics such as gene annotation, disease integration, phenotype ontology, data integration, and the use of semantic web technologies in knowledge management. |
| Domain | Life Sciences |
| Field | Biochemistry, Genetics and Molecular Biology |
| OpenAlex ID | t11710 |
| Works | 110 |

## Topic papers all

Showing 15 of 110.

- [Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature](https://scholariq.org/papers/automatic-parcellation-of-human-cortical-gyri-and-sulci-using-standard/)
- [PhenoScanner V2: an expanded tool for searching human genotype–phenotype associations](https://scholariq.org/papers/phenoscanner-v2-an-expanded-tool-for-searching-human-genotype-phenotype/)
- [The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments](https://scholariq.org/papers/the-brain-imaging-data-structure-a-format-for-organizing-and-describing-outputs/)
- [Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records](https://scholariq.org/papers/deep-patient-an-unsupervised-representation-to-predict-the-future-of-patients/)
- [PhenoScanner: a database of human genotype–phenotype associations](https://scholariq.org/papers/phenoscanner-a-database-of-human-genotype-phenotype-associations/)
- [DrugBank 6.0: the DrugBank Knowledgebase for 2024](https://scholariq.org/papers/drugbank-6-0-the-drugbank-knowledgebase-for-2024/)
- [SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse](https://scholariq.org/papers/syngo-an-evidence-based-expert-curated-knowledge-base-for-the-synapse/)
- [Understanding multicellular function and disease with human tissue-specific networks](https://scholariq.org/papers/understanding-multicellular-function-and-disease-with-human-tissue-specific/)
- [Clinical information extraction applications: A literature review](https://scholariq.org/papers/clinical-information-extraction-applications-a-literature-review/)
- [Error bars in experimental biology](https://scholariq.org/papers/error-bars-in-experimental-biology/)
- [The ExAC browser: displaying reference data information from over 60 000 exomes](https://scholariq.org/papers/the-exac-browser-displaying-reference-data-information-from-over-60-000-exomes/)
- [Development of a highly sensitive search strategy for the retrieval of reports of controlled trials using PubMed](https://scholariq.org/papers/development-of-a-highly-sensitive-search-strategy-for-the-retrieval-of-reports/)
- [The Human Phenotype Ontology in 2017](https://scholariq.org/papers/the-human-phenotype-ontology-in-2017/)
- [Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources](https://scholariq.org/papers/expansion-of-the-human-phenotype-ontology-hpo-knowledge-base-and-resources/)
- [Constructing biological knowledge bases by extracting information from text sources.](https://scholariq.org/papers/constructing-biological-knowledge-bases-by-extracting-information-from-text/)

## Topic primary papers

Showing 15 of 42.

- [Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature](https://scholariq.org/papers/automatic-parcellation-of-human-cortical-gyri-and-sulci-using-standard/)
- [Clinical information extraction applications: A literature review](https://scholariq.org/papers/clinical-information-extraction-applications-a-literature-review/)
- [Error bars in experimental biology](https://scholariq.org/papers/error-bars-in-experimental-biology/)
- [The Human Phenotype Ontology in 2017](https://scholariq.org/papers/the-human-phenotype-ontology-in-2017/)
- [Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources](https://scholariq.org/papers/expansion-of-the-human-phenotype-ontology-hpo-knowledge-base-and-resources/)
- [Constructing biological knowledge bases by extracting information from text sources.](https://scholariq.org/papers/constructing-biological-knowledge-bases-by-extracting-information-from-text/)
- [Citationchaser: A tool for transparent and efficient forward and backward citation chasing in systematic searching](https://scholariq.org/papers/citationchaser-a-tool-for-transparent-and-efficient-forward-and-backward/)
- [The Ontology for Biomedical Investigations](https://scholariq.org/papers/the-ontology-for-biomedical-investigations/)
- [Standardizing nomenclature in regional anesthesia: an ASRA-ESRA Delphi consensus study of abdominal wall, paraspinal, and chest wall blocks](https://scholariq.org/papers/standardizing-nomenclature-in-regional-anesthesia-an-asra-esra-delphi-consensus/)
- [The Brain Atlas Concordance Problem: Quantitative Comparison of Anatomical Parcellations](https://scholariq.org/papers/the-brain-atlas-concordance-problem-quantitative-comparison-of-anatomical/)
- [Construction of a Bayesian network for mammographic diagnosis of breast cancer](https://scholariq.org/papers/construction-of-a-bayesian-network-for-mammographic-diagnosis-of-breast-cancer/)
- [CBLUE: A Chinese Biomedical Language Understanding Evaluation Benchmark](https://scholariq.org/papers/cblue-a-chinese-biomedical-language-understanding-evaluation-benchmark/)
- [BioTop: An upper domain ontology for the life sciences](https://scholariq.org/papers/biotop-an-upper-domain-ontology-for-the-life-sciences/)
- [GenCLiP 3: mining human genes’ functions and regulatory networks from PubMed based on co-occurrences and natural language processing](https://scholariq.org/papers/genclip-3-mining-human-genes-functions-and-regulatory-networks-from-pubmed-based/)
- [CREATING KNOWLEDGE REPOSITORIES FROM BIOMEDICAL REPORTS: THE MEDSYNDIKATE TEXT MINING SYSTEM](https://scholariq.org/papers/creating-knowledge-repositories-from-biomedical-reports-the-medsyndikate-text/)

---
Source: ScholarIQ — public research metadata, principally OpenAlex. See https://scholariq.org/sources/ for provenance and https://scholariq.org/methodology/ for what these figures mean.