PubTator central: automated concept annotation for biomedical full text articles

Convolutional Neural Networks for Sentence Classification

Kim, Y. (2014) · Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP) · doi:10.3115/v1/d14-1181 · Cited by 14,831 · see citing works

NCBI Disease Corpus: A Resource for Disease Name Recognition and Concept Normalization

Dogan, R., Leaman, R., & Lu, Z.-Y. (2014) · Journal of Biomedical Informatics · doi:10.1016/j.jbi.2013.12.006 · Cited by 994 · see citing works

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

Li, J., Sun, Y., Johnson, R. J., Sciaky, D., Wei, C.-H., Leaman, R., Davis, A. P., Mattingly, C. J., Wiegers, T. C., & Lu, Z. (2016) · Database · doi:10.1093/database/baw068 · Cited by 857 · see citing works

The Cellosaurus, a Cell-Line Knowledge Resource

Bairoch, A. (2018) · Journal of Biomolecular Techniques JBT · doi:10.7171/jbt.18-2902-002 · Cited by 807 · see citing works

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

Wei, C.-H., Kao, H. Y., & Lu, Z. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt441 · Cited by 567 · see citing works

DNorm: disease name normalization with pairwise learning to rank

Leaman, R., Islamaj, R., & Lu, Z. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt474 · Cited by 484 · see citing works

The CHEMDNER corpus of chemicals and drugs and its annotation principles

Krallinger, M., Rabal, O., Leitner, F., Vázquez, M., Salgado, D., Lu, Z., Leaman, R., Lu, Y., Ji, D., Lowe, D. M., et al. (2015) · Journal of Cheminformatics · doi:10.1186/1758-2946-7-s1-s2 · Cited by 406 · see citing works

LINNAEUS: A species name identification system for biomedical literature

Gerner, M., Nenadić, G., & Bergman, C. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-85 · Cited by 337 · see citing works

Overview of BioCreative II gene normalization

Morgan, A. A., Lu, Z., Wang, X., Cohen, A. M., Fluck, J., Ruch, P., Divoli, A., Fundel, K., Leaman, R., Hakenberg, J., et al. (2008) · Genome biology · doi:10.1186/gb-2008-9-s2-s3 · Cited by 327 · see citing works

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

Leaman, R., & Lu, Z.-Y. (2016) · Bioinform. · doi:10.1093/bioinformatics/btw343 · Cited by 297 · see citing works

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

Wei, C.-H., Kao, H., & Lu, Z. (2015) · BioMed Research International · doi:10.1155/2015/918710 · Cited by 208 · see citing works

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task

Wei, C.-H., Peng, Y., Leaman, R., Davis, A. P., Mattingly, C. J., Li, J., Wiegers, T. C., & Lu, Z. (2016) · Database · doi:10.1093/database/baw032 · Cited by 198 · see citing works

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

Westergaard, D., Stærfeldt, H., Tønsberg, C., Jensen, L. J., & Brunak, S. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005962 · Cited by 198 · see citing works

BioC: a minimalist approach to interoperability for biomedical text processing

Comeau, D. C., Islamaj, R., Ciccarese, P., Cohen, K. B., Krallinger, M., Leitner, F., Lu, Z., Peng, Y., Rinaldi, F., Torii, M., et al. (2013) · Database · doi:10.1093/database/bat064 · Cited by 176 · see citing works

The structural and content aspects of abstracts versus bodies of full text journal articles are different

Cohen, K. B., Johnson, H. L., Verspoor, K., Roeder, C., & Hunter, L. E. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-492 · Cited by 174 · see citing works

Text mining for the biocuration workflow

Hirschman, L., Burns, G., Krallinger, M., Arighi, C. N., Cohen, K. B., Valencia, A., Wu, C. H., Chatr‐aryamontri, A., Dowell, K. G., Huala, E., et al. (2012) · Database · doi:10.1093/database/bas020 · Cited by 172 · see citing works

tmVar: a text mining approach for extracting sequence variants in biomedical literature

Wei, C.-H., Harris, B., Kao, H., & Lu, Z. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt156 · Cited by 168 · see citing works

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC

Allot, A., Peng, Y., Wei, C.-H., Lee, K., Phan, L. D., & Lu, Z. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky355 · Cited by 141 · see citing works

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study

Poux, S., Arighi, C. N., Magrane, M., Bateman, A., Wei, C.-H., Lu, Z., Boutet, E., Bye-A-Jee, H., Famiglietti, M. L., Roechert, B., et al. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx439 · Cited by 135 · see citing works

A global network of biomedical relationships derived from text

Percha, B., & Altman, R. B. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty114 · Cited by 131 · see citing works

Abbreviation definition identification based on automatic precision estimates

Sohn, S., Comeau, D. C., Kim, W. B., & Wilbur, W. J. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-402 · Cited by 120 · see citing works

Is searching full text more effective than searching abstracts?

Lin, J. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-46 · Cited by 116 · see citing works

BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature

Lee, S., Kim, D., Lee, K., Choi, J., Kim, S., Jeon, M., Lim, S., Choi, D., Kim, S., Tan, A. C., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0164680 · Cited by 101 · see citing works

tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine

Wei, C.-H., Phan, L. D., Feltz, J., et al. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx541 · Cited by 97 · see citing works

Text mining genotype-phenotype relationships from biomedical literature for database curation and precision medicine

Singhal, A., Simmons, M., & Lu, Z. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005017 · Cited by 96 · see citing works

Cross-species gene normalization by species inference

Wei, C.-H., & Kao, H. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-s8-s5 · Cited by 88 · see citing works

SR4GN: A Species Recognition Software Tool for Gene Normalization

Wei, C.-H., Kao, H., & Lu, Z. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038460 · Cited by 87 · see citing works

PMC text mining subset in BioC: about three million full-text articles and growing

Comeau, D. C., Wei, C.-H., Islamaj, R., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz070 · Cited by 84 · see citing works

Argo: an integrative, interactive, text mining-based workbench supporting curation

Rak, R., Rowley, A., Black, W. J., et al. (2012) · Database · doi:10.1093/database/bas010 · Cited by 77 · see citing works

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II

Lu, Z., & Hirschman, L. (2012) · Database · doi:10.1093/database/bas043 · Cited by 73 · see citing works

12 years on – Is the NLM medical text indexer still useful and relevant?

Mork, J., Aronson, A., & Demner-Fushman, D. (2017) · Journal of Biomedical Semantics · doi:10.1186/s13326-017-0113-5 · Cited by 73 · see citing works

GeneView: a comprehensive semantic search engine for PubMed

Thomas, P. E., Starlinger, J., Vowinkel, A., Arzt, S., & Leser, U. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks563 · Cited by 70 · see citing works

DiMeX: A Text Mining System for Mutation-Disease Association Extraction

Mahmood, A. S. M. A., Wu, T.-J., Mazumder, R., & Vijay‐Shanker, K. (2016) · PLoS ONE · doi:10.1371/journal.pone.0152725 · Cited by 67 · see citing works

LION LBD: a literature-based discovery system for cancer biology

Pyysalo, S., Baker, S., Ali, I., Haselwimmer, S., Shah, T., Young, A., Guo, Y., Högberg, J., Stenius, U., Narita, M., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty845 · Cited by 65 · see citing works

Thalia: semantic search engine for biomedical abstracts

Soto, A. J., Przybyła, P., & Ananiadou, S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty871 · Cited by 60 · see citing works

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Singhal, A., Leaman, R., Catlett, N., Lemberger, T., McEntyre, J., Polson, S., Xenarios, I., Arighi, C., & Lu, Z. (2016) · Database · doi:10.1093/database/baw161 · Cited by 48 · see citing works

Scaling up data curation using deep learning: An application to literature triage in genomic variation resources

Lee, K., Famiglietti, M. L., McMahon, A., Wei, C.-H., MacArthur, J. A. L., Poux, S., Breuza, L., Bridge, A., Cunningham, F., Xenarios, I., et al. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006390 · Cited by 47 · see citing works

Literature mining of genetic variants for curation: quantifying the importance of supplementary material

Yepes, A. J., & Verspoor, K. M. (2014) · Database · doi:10.1093/database/bau003 · Cited by 45 · see citing works

Hybrid curation of gene–mutation relations combining automated extraction and crowdsourcing

Burger, J. D., Doughty, E., Khare, R., Wei, C.-H., Mishra, R., Aberdeen, J. S., Tresner‐Kirsch, D., Wellner, B., Kann, M. G., Lu, Z., et al. (2014) · Database · doi:10.1093/database/bau094 · Cited by 44 · see citing works

BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations

Lee, K., Lee, S., Park, S., et al. (2016) · Database · doi:10.1093/database/baw043 · Cited by 43 · see citing works

Results of the fifth edition of the BioASQ Challenge

Nentidis, A., Bougiatiotis, K., Krithara, A., Παλιούρας, Γ., & Kakadiaris, I. A. (2017) · doi:10.18653/v1/w17-2306 · Cited by 33 · see citing works

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources

Huang, L., ROSS, K. E., Baffi, T. R., Drabkin, H., Kochut, K., Ruan, Z., D’Eustachio, P., McSkimming, D. I., Arighi, C. N., Chen, C., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-24457-1 · Cited by 30 · see citing works

PubTerm: a web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records

Garcia‐Pelaez, J., Rodríguez, D., Medina-Molina, R., García‐Rivas, G., Carlos Jerjes-Sánchez, D., & Treviño, V. (2018) · Database · doi:10.1093/database/bay137 · Cited by 26 · see citing works

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data

Venkatesan, A., Kim, J.-H., Talo, F., Ide‐Smith, M., Gobeill, J., Carter, J., Batista-Navarro, R., Ananiadou, S., Ruch, P., & McEntyre, J. (2016) · Wellcome Open Research · doi:10.12688/wellcomeopenres.10210.1 · Cited by 26 · see citing works

SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedical Text

Wei, C.-H., Leaman, R., & Lu, Z. (2015) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2015.2422651 · Cited by 24 · see citing works

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data

Venkatesan, A., Kim, J.-H., Talo, F., Ide‐Smith, M., Gobeill, J., Carter, J., Batista-Navarro, R., Ananiadou, S., Ruch, P., & McEntyre, J. (2017) · Wellcome Open Research · doi:10.12688/wellcomeopenres.10210.2 · Cited by 24 · see citing works

A Proteomic Study of Human Merkel Cell Carcinoma

Shao, Q. (2013) · Journal of Proteomics & Bioinformatics · doi:10.4172/jpb.1000291 · Cited by 23 · see citing works

HiPub: translating PubMed and PMC texts to networks for knowledge discovery

Lee, K., Shin, W., Kim, B., et al. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw511 · Cited by 20 · see citing works

A PubMed-wide study of endometriosis

Liu, J., & Zhao, M. (2016) · Genomics · doi:10.1016/j.ygeno.2016.10.003 · Cited by 19 · see citing works

Configurable web-services for biomedical document annotation

Matos, S. (2018) · Journal of Cheminformatics · doi:10.1186/s13321-018-0317-4 · Cited by 9 · see citing works

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system

Peng, Y., Tudor, C. O., Torii, M., Wu, C. H., & Vijay‐Shanker, K. (2014) · Database · doi:10.1093/database/bau038 · Cited by 8 · see citing works

Evaluation of the Performance of BioNLP Tools for Discovering Causal Genes in Terms with Pathway Enrichment

Qin, X., Wang, S., Wu, Y., et al. (2018) · Journal of Physics Conference Series · doi:10.1088/1742-6596/1069/1/012037 · Cited by 3 · see citing works

LitCovid: an open database of COVID-19 literature

Chen, Q., Allot, A., & Lu, Z. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa952 · Cited by 253 · see citing works

Efficient Attentions for Long Document Summarization

Huang, L., Cao, S., Parulian, N., Ji, H., & Wang, L. (2021) · Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies · doi:10.18653/v1/2021.naacl-main.112 · Cited by 146 · see citing works

LitSuggest: a web-based system for literature recommendation and curation using machine learning

Allot, A., Lee, K., Chen, Q., Luo, L., & Lu, Z. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab326 · Cited by 61 · see citing works

Protection of the human gene research literature from contract cheating organizations known as research paper mills

Byrne, J. A., Park, Y., Richardson, R. A. K., Pathmendra, P., Sun, M., & Stoeger, T. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1139 · Cited by 46 · see citing works

COVID-19 research risks ignoring important host genes due to pre-established research patterns

Stoeger, T., & Nunes Amaral, L. A. (2020) · eLife · doi:10.7554/elife.61981 · Cited by 30 · see citing works

Deep learning with sentence embeddings pre-trained on biomedical corpora improves the performance of finding similar sentences in electronic medical records

Chen, Q., Du, J., Kim, S., Wilbur, W. J., & Lu, Z. (2020) · BMC Medical Informatics and Decision Making · doi:10.1186/s12911-020-1044-0 · Cited by 19 · see citing works

SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts

Gobeill, J., Caucheteur, D., Michel, P.-A., Mottin, L., Pasche, E., & Ruch, P. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa328 · Cited by 20 · see citing works

Artificial Intelligence Clinical Evidence Engine for Automatic Identification, Prioritization, and Extraction of Relevant Clinical Oncology Research

Saiz, F. S., Sanders, C., Stevens, R., Nielsen, R., Britt, M., Yuravlivker, L., Preininger, A. M., & Jackson, G. P. (2021) · JCO Clinical Cancer Informatics · doi:10.1200/cci.20.00087 · Cited by 17 · see citing works

Microevolutionary dynamics of eccDNA in Chinese hamster ovary cells grown in fed-batch cultures under control and lactate-stressed conditions

Chitwood, D. G., Wang, Q., Klaubert, S. R., Green, K., Wu, C. H., Harcum, S. W., & Saski, C. A. (2023) · Scientific Reports · doi:10.1038/s41598-023-27962-0 · Cited by 12 · see citing works

iStarJSON: A Lightweight Data-Format for i* Models.

Franco-Bedoya, O., Ameller, D., Costal, D., et al. (2016) · UPCommons institutional repository (Universitat Politècnica de Catalunya) · Cited by 2 · see citing works

Application study on JSON data exchange format in integration of Heterogeneous System

Shen, B. (2012) · Railway Computer Application · Cited by 2 · see citing works

Model of data for subsystem of spectroscopy diagnostic

Oleg, F. (2013) · International Conference on Experience of Designing and Applications of CAD Systems in Microelectronics

ELCC 2022 Highlights Podcast

Giles, D. R. (2022) · doi:10.55788/66e10816

Research of GIS data exchange method based on JSON

Feng, H. (2010) · Cehui kexue · Cited by 3 · see citing works