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One tagger, many uses: Illustrating the power of ontologies in dictionary-based named entity recognition

https://doi.org/10.1101/067132
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/978-3-319-31744-1_66openalex-snapshot
A Comprehensive Comparison of Two MEDLINE Annotators for Disease and Gene Linkage: Sometimes Less is More
inferredcites →https://doi.org/10.1016/j.ymeth.2014.11.020openalex-snapshot
DISEASES: Text mining and data integration of disease–gene associations
inferredcites →https://doi.org/10.1016/s1574-1400(08)00012-1openalex-snapshot
PubChem: Integrated Platform of Small Molecules and Biological Activities
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/nbt0609-508openalex-snapshot
Reflect: augmented browsing for the life scientist
inferredcites →https://doi.org/10.1093/bioinformatics/btv045openalex-snapshot
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life
inferredcites →https://doi.org/10.1093/database/bau012openalex-snapshot
COMPARTMENTS: unification and visualization of protein subcellular localization evidence
inferredcites →https://doi.org/10.1093/database/baw005openalex-snapshot
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation
inferredcites →https://doi.org/10.1093/database/baw032openalex-snapshot
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
inferredcites →https://doi.org/10.1093/nar/gkt1207openalex-snapshot
STITCH 4: integration of protein–chemical interactions with user data
inferredcites →https://doi.org/10.1093/nar/gkt1274openalex-snapshot
RefSeq microbial genomes database: new representation and annotation strategy
inferredcites →https://doi.org/10.1093/nar/gku1003openalex-snapshot
STRING v10: protein–protein interaction networks, integrated over the tree of life
inferredcites →https://doi.org/10.1093/nar/gku1010openalex-snapshot
Ensembl 2015
inferredcites →https://doi.org/10.1093/nar/gku1011openalex-snapshot
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
inferredcites →https://doi.org/10.1093/nar/gku1068openalex-snapshot
BRENDA in 2015: exciting developments in its 25th year of existence
inferredcites →https://doi.org/10.1093/nar/gku1127openalex-snapshot
Type material in the NCBI Taxonomy Database
inferredcites →https://doi.org/10.1093/nar/gku989openalex-snapshot
UniProt: a hub for protein information
inferredcites →https://doi.org/10.1093/nar/gkv1075openalex-snapshot
The SIDER database of drugs and side effects
inferredcites →https://doi.org/10.1136/amiajnl-2013-001708openalex-snapshot
Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text
inferredcites →https://doi.org/10.1186/1471-2105-12-s8-s2openalex-snapshot
The gene normalization task in BioCreative III
inferredcites →https://doi.org/10.1186/2041-1480-4-43openalex-snapshot
The environment ontology: contextualising biological and biomedical entities
inferredcites →https://doi.org/10.1371/journal.pone.0065390openalex-snapshot
The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
inferredcites →https://doi.org/10.18653/v1/w16-3006openalex-snapshot
A dictionary- and rule-based system for identification of bacteria and habitats in text
inferredcites →https://doi.org/10.3115/v1/p15-4016openalex-snapshot
Sharing annotations better: RESTful Open Annotation
inferredcites →https://doi.org/10.7717/peerj.1054openalex-snapshot
Comprehensive comparison of large-scale tissue expression datasets

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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An integrated pipeline model for biomedical entity alignment
inferred← citeshttps://doi.org/10.1016/j.csbj.2025.06.025openalex-snapshot
Darling (v2.0): Mining disease-related databases for the detection of biomedical entity associations
inferred← citeshttps://doi.org/10.1038/s41598-020-57716-1openalex-snapshot
Ontology-driven integrative analysis of omics data through Onassis
inferred← citeshttps://doi.org/10.1093/bioadv/vbae116openalex-snapshot
CoNECo: a Corpus for Named Entity recognition and normalization of protein Complexes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btad369openalex-snapshot
S1000: a better taxonomic name corpus for biomedical information extraction
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae402openalex-snapshot
Improving dictionary-based named entity recognition with deep learning
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae552openalex-snapshot
STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae613openalex-snapshot
Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition
inferred← citeshttps://doi.org/10.1093/database/baae095openalex-snapshot
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature
inferred← citeshttps://doi.org/10.1093/nar/gkaa1074openalex-snapshot
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
inferred← citeshttps://doi.org/10.3389/fmars.2022.940844openalex-snapshot
Automating the Curation Process of Historical Literature on Marine Biodiversity Using Text Mining: The DECO Workflow
inferred← citeshttps://doi.org/10.3390/microorganisms10020293openalex-snapshot
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types
inferred← citeshttps://doi.org/10.7554/elife.84919openalex-snapshot
Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records
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