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Expanding a Database-derived Biomedical Knowledge Graph via Multi-relation Extraction from Biomedical Abstracts

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What this work says

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

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Growth rates of modern science: A bibliometric analysis based on the number of publications and cited references

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Snorkel: rapid training data creation with weak supervision.

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Comparative experiments on learning information extractors for proteins and their interactions

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A Proteome-Scale Map of the Human Interactome Network

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The EU-ADR corpus: Annotated drugs, diseases, targets, and their relationships

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LGscore: A method to identify disease-related genes using biological literature and Google data

inferredcites →https://doi.org/10.1016/j.jbi.2015.01.006openalex-snapshot

HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways

inferredcites →https://doi.org/10.1016/j.jbi.2015.08.008openalex-snapshot

PKDE4J: Entity and relation extraction for public knowledge discovery

inferredcites →https://doi.org/10.1016/j.knosys.2018.11.020openalex-snapshot

Feature assisted stacked attentive shortest dependency path based Bi-LSTM model for protein–protein interaction

inferredcites →https://doi.org/10.1016/j.neunet.2014.09.003openalex-snapshot

Deep learning in neural networks: An overview

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/j.ymeth.2015.01.015openalex-snapshot

Application of text mining in the biomedical domain

inferredcites →https://doi.org/10.1038/536016aopenalex-snapshot

Legal confusion threatens to slow data science

inferredcites →https://doi.org/10.1038/nrg1768openalex-snapshot

Literature mining for the biologist: from information retrieval to biological discovery

inferredcites →https://doi.org/10.1093/bib/bbn043openalex-snapshot

Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

inferredcites →https://doi.org/10.1093/bioinformatics/btl616openalex-snapshot

RelEx—Relation extraction using dependency parse trees

inferredcites →https://doi.org/10.1093/bioinformatics/btm229openalex-snapshot

Manual curation is not sufficient for annotation of genomic databases

inferredcites →https://doi.org/10.1093/bioinformatics/btr042openalex-snapshot

GeneTUKit: a software for document-level gene normalization

inferredcites →https://doi.org/10.1093/bioinformatics/btt474openalex-snapshot

DNorm: disease name normalization with pairwise learning to rank

inferredcites →https://doi.org/10.1093/bioinformatics/btv476openalex-snapshot

Large-scale extraction of gene interactions from full-text literature using DeepDive

inferredcites →https://doi.org/10.1093/bioinformatics/btw503openalex-snapshot

DTMiner: identification of potential disease targets through biomedical literature mining

inferredcites →https://doi.org/10.1093/bioinformatics/bty114openalex-snapshot

A global network of biomedical relationships derived from text

inferredcites →https://doi.org/10.1093/bioinformatics/btz490openalex-snapshot

CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision

inferredcites →https://doi.org/10.1093/bioinformatics/btz682openalex-snapshot

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

inferredcites →https://doi.org/10.1093/database/bas037openalex-snapshot

Collaborative biocuration--text-mining development task for document prioritization for curation

inferredcites →https://doi.org/10.1093/database/bas052openalex-snapshot

PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

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/baw068openalex-snapshot

BioCreative V CDR task corpus: a resource for chemical disease relation extraction

inferredcites →https://doi.org/10.1093/database/bay060openalex-snapshot

Chemical–gene relation extraction using recursive neural network

inferredcites →https://doi.org/10.1093/database/bay066openalex-snapshot

Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings

inferredcites →https://doi.org/10.1093/database/bay073openalex-snapshot

Extracting chemical–protein relations with ensembles of SVM and deep learning models

inferredcites →https://doi.org/10.1093/database/bay102openalex-snapshot

Extracting chemical–protein relations using attention-based neural networks

inferredcites →https://doi.org/10.1093/database/bay108openalex-snapshot

LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task

inferredcites →https://doi.org/10.1093/database/baz095openalex-snapshot

Extraction of chemical–protein interactions from the literature using neural networks and narrow instance representation

inferredcites →https://doi.org/10.1093/nar/gkt441openalex-snapshot

PubTator: a web-based text mining tool for assisting biocuration

inferredcites →https://doi.org/10.1093/nar/gkv383openalex-snapshot

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

inferredcites →https://doi.org/10.1093/nar/gkw1133openalex-snapshot

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

inferredcites →https://doi.org/10.1093/nar/gkx1037openalex-snapshot

DrugBank 5.0: a major update to the DrugBank database for 2018

inferredcites →https://doi.org/10.1093/nar/gkx462openalex-snapshot

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes

inferredcites →https://doi.org/10.1101/385617openalex-snapshot

Drug repurposing through joint learning on knowledge graphs and literature

inferredcites →https://doi.org/10.1109/5254.708428openalex-snapshot

Support vector machines

inferredcites →https://doi.org/10.1109/bibm.2015.7359766openalex-snapshot

A new method for prioritizing drug repositioning candidates extracted by literature-based discovery

inferredcites →https://doi.org/10.1109/tcbb.2014.2372765openalex-snapshot

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information

inferredcites →https://doi.org/10.1126/science.1257601openalex-snapshot

Uncovering disease-disease relationships through the incomplete interactome

inferredcites →https://doi.org/10.1145/3209889.3209898openalex-snapshot

Snorkel MeTaL

inferredcites →https://doi.org/10.1177/0165551516673485openalex-snapshot

Extraction of protein–protein interactions (PPIs) from the literature by deep convolutional neural networks with various feature embeddings

inferredcites →https://doi.org/10.1186/1471-2105-10-s2-s6openalex-snapshot

Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text

inferredcites →https://doi.org/10.1186/1471-2105-12-s8-s5openalex-snapshot

Cross-species gene normalization by species inference

inferredcites →https://doi.org/10.1186/1471-2105-14-181openalex-snapshot

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

inferredcites →https://doi.org/10.1186/1471-2105-8-50openalex-snapshot

BioInfer: a corpus for information extraction in the biomedical domain

inferredcites →https://doi.org/10.1186/1471-2105-9-405openalex-snapshot

iRefIndex: A consolidated protein interaction database with provenance

inferredcites →https://doi.org/10.1186/1471-2105-9-s3-s6openalex-snapshot

Comparative analysis of five protein-protein interaction corpora

inferredcites →https://doi.org/10.1186/s12859-015-0472-9openalex-snapshot

Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research

inferredcites →https://doi.org/10.1186/s12859-018-2048-yopenalex-snapshot

The research on gene-disease association based on text-mining of PubMed

inferredcites →https://doi.org/10.1186/s12859-018-2103-8openalex-snapshot

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature

inferredcites →https://doi.org/10.1186/s12859-019-2634-7openalex-snapshot

Analyzing a co-occurrence gene-interaction network to identify disease-gene association

inferredcites →https://doi.org/10.1186/s12859-019-2873-7openalex-snapshot

Knowledge-guided convolutional networks for chemical-disease relation extraction

inferredcites →https://doi.org/10.1186/s13326-017-0168-3openalex-snapshot

Exploiting graph kernels for high performance biomedical relation extraction

inferredcites →https://doi.org/10.1371/journal.pcbi.1000943openalex-snapshot

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases

inferredcites →https://doi.org/10.1371/journal.pcbi.1004630openalex-snapshot

Text Mining for Protein Docking

inferredcites →https://doi.org/10.1371/journal.pcbi.1005962openalex-snapshot

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

inferredcites →https://doi.org/10.1371/journal.pone.0084912openalex-snapshot

Graph Theory Enables Drug Repurposing – How a Mathematical Model Can Drive the Discovery of Hidden Mechanisms of Action

inferredcites →https://doi.org/10.1371/journal.pone.0200699openalex-snapshot

Automatic extraction of gene-disease associations from literature using joint ensemble learning

inferredcites →https://doi.org/10.1371/journal.pone.0213090openalex-snapshot

An analysis and metric of reusable data licensing practices for biomedical resources

inferredcites →https://doi.org/10.14778/3157794.3157797openalex-snapshot

Snorkel

inferredcites →https://doi.org/10.3115/1690219.1690287openalex-snapshot

Distant supervision for relation extraction without labeled data

inferredcites →https://doi.org/10.3115/v1/p14-5010openalex-snapshot

The Stanford CoreNLP Natural Language Processing Toolkit

inferredcites →https://doi.org/10.63317/2frw8qrccomtopenalex-snapshot

Revisiting Distant Supervision for Relation Extraction

inferredcites →https://doi.org/10.7554/elife.26726openalex-snapshot

Systematic integration of biomedical knowledge prioritizes drugs for repurposing

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.

inferred← citeshttps://doi.org/10.1016/j.csbj.2020.05.017openalex-snapshot

Constructing knowledge graphs and their biomedical applications

inferred← citeshttps://doi.org/10.1093/bib/bbaa357openalex-snapshot

Topological network measures for drug repositioning

inferred← citeshttps://doi.org/10.1093/nar/gkab543openalex-snapshot

CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.