# Biomedical Flat and Nested Named Entity Recognition: Methods, Challenges, and Advances
## 3 Deep Learning Methods for Flat NER
\begin{table}
\begin{tabular}{l c c c} \hline \hline
**Dataset** & **Norm \({}^{*}\)** & **URL** & **Ref.** \\ \hline Flat NER & & & \\ \hline Multi-Type & & & \\ \hline BioRED & ✓ & [[https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/](https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/)]([https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/](https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/)) & [43] \\ MedMention & ✓ & [[https://github.com/chanzuckerberg/MedMentions](https://github.com/chanzuckerberg/MedMentions)]([https://github.com/chanzuckerberg/MedMentions](https://github.com/chanzuckerberg/MedMentions)) & [44] \\ CRAFT & ✓ & [[http://bionlp-corpora.sourceforge.net/CRAFT/](http://bionlp-corpora.sourceforge.net/CRAFT/)]([http://bionlp-corpora.sourceforge.net/CRAFT/](http://bionlp-corpora.sourceforge.net/CRAFT/)) & [45] \\ JNLPBA & & [[https://github.com/openbiocorpora/jnlpba](https://github.com/openbiocorpora/jnlpba)]([https://github.com/openbiocorpora/jnlpba](https://github.com/openbiocorpora/jnlpba)) \({}^{*}\) & [46] \\ CellFinder & & [[https://github.com/openbiocorpora/cellular](https://github.com/openbiocorpora/cellular)]([https://github.com/openbiocorpora/cellular](https://github.com/openbiocorpora/cellular)) \({}^{*}\) & [47] \\ miRNA & & [[https://www.sciaf.tauhwoferde/mirna-corpora.html](https://www.sciaf.tauhwoferde/mirna-corpora.html)]([https://www.sciaf.tauhwoferde/mirna-corpora.html](https://www.sciaf.tauhwoferde/mirna-corpora.html)) & [48] \\ Nagel & & [[https://sourceforge.net/projects/bionlp-corpora/files/](https://sourceforge.net/projects/bionlp-corpora/files/)]([https://sourceforge.net/projects/bionlp-corpora/files/](https://sourceforge.net/projects/bionlp-corpora/files/)) & [49] \\ ProteinResidue/ & & & [50] \\ GREC & & [[http://www.nacentra.cuk/GREC/](http://www.nacentra.cuk/GREC/)]([http://www.nacentra.cuk/GREC/](http://www.nacentra.cuk/GREC/)) & [51] \\ BC5 CDR & ✓ & [[https://github.com/openbiocorpora/biocreutive-v-cdr](https://github.com/openbiocorpora/biocreutive-v-cdr)]([https://github.com/openbiocorpora/biocreutive-v-cdr](https://github.com/openbiocorpora/biocreutive-v-cdr)) \({}^{*}\) & [51] \\ DrugProt & & [[https://zenodo.org/records/5119892](https://zenodo.org/records/5119892)]([https://zenodo.org/records/5119892](https://zenodo.org/records/5119892)) & [52] \\ tmVar 3.0 & ✓ & [[https://github.com/ncbi/tmVar3](https://github.com/ncbi/tmVar3) Tab=readme-ov-file]([https://github.com/ncbi/tmVar3](https://github.com/ncbi/tmVar3) Tab=readme-ov-file) & [53] \\ \hline Gene/Protein & & & \\ \hline BC2 GM & ✓ & [[https://github.com/openbiocorpora/biocreative-ii-gn](https://github.com/openbiocorpora/biocreative-ii-gn)]([https://github.com/openbiocorpora/biocreative-ii-gn](https://github.com/openbiocorpora/biocreative-ii-gn)) \({}^{*}\) & [54] \\ DECA & ✓ & [[http://www.nacentra.cuk/deca/](http://www.nacentra.cuk/deca/)]([http://www.nacentra.cuk/deca/](http://www.nacentra.cuk/deca/)) & [55] \\ GETIM & & [[https://getn-project.sourceforge.net/](https://getn-project.sourceforge.net/)]([https://getn-project.sourceforge.net/](https://getn-project.sourceforge.net/)) & [56] \\ LocText & ✓ & [[https://github.com/Rostlab/LocText](https://github.com/Rostlab/LocText)]([https://github.com/Rostlab/LocText](https://github.com/Rostlab/LocText)) & [57] \\ FSU-PRGE & & [[https://julield.de/Resources/FSU_PRGE.html](https://julield.de/Resources/FSU_PRGE.html)]([https://julield.de/Resources/FSU_PRGE.html](https://julield.de/Resources/FSU_PRGE.html)) & [58] \\ NLM-Gene & ✓ & [[https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMGene/](https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMGene/)]([https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMGene/](https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMGene/)) & [59] \\ \hline Chemical & & & \\ \hline SCAI Chem & ✓ & [[https://www.sciaf.raunhofer.de/chem-corpora.html](https://www.sciaf.raunhofer.de/chem-corpora.html)]([https://www.sciaf.raunhofer.de/chem-corpora.html](https://www.sciaf.raunhofer.de/chem-corpora.html)) & [60] \\ DDI & & [[https://github.com/isegura/DDICorpus](https://github.com/isegura/DDICorpus)]([https://github.com/isegura/DDICorpus](https://github.com/isegura/DDICorpus)) & [61] \\ BC4 CHEMD & ✓ & [[https://github.com/bionlp-hzau/BioNLP-Corpus](https://github.com/bionlp-hzau/BioNLP-Corpus)]([https://github.com/bionlp-hzau/BioNLP-Corpus](https://github.com/bionlp-hzau/BioNLP-Corpus)) \({}^{*}\) & [62] \\ NLM-Chem & ✓ & [[https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMChem/](https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMChem/)]([https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMChem/](https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMChem/)) & [63] \\ \hline Disease & & & \\ \hline SCAI disease & & [[https://www.sciaf.tauhwofer.de/disease-ae-corpus.html](https://www.sciaf.tauhwofer.de/disease-ae-corpus.html)]([https://www.sciaf.tauhwofer.de/disease-ae-corpus.html](https://www.sciaf.tauhwofer.de/disease-ae-corpus.html)) & [64] \\ NCBI disease & ✓ & [[http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/](http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/)]([http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/](http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/DISEASE/)) & [65] \\ \hline Species & & & \\ \hline LINNAEUS & ✓ & [[http://linnaeus.sourceforge.net/](http://linnaeus.sourceforge.net/)]([http://linnaeus.sourceforge.net/](http://linnaeus.sourceforge.net/)) & [66] \\ Species-1000 & ✓ & [[https://jensenlab.org/resources/s1000/](https://jensenlab.org/resources/s1000/)]([https://jensenlab.org/resources/s1000/](https://jensenlab.org/resources/s1000/)) & [67] \\ \hline Variant & & & \\ \hline SNP corpus & ✓ & [[https://www.sciaf.tauhwofer.de/snp-normalization-corpus.html](https://www.sciaf.tauhwofer.de/snp-normalization-corpus.html)]([https://www.sciaf.tauhwofer.de/snp-normalization-corpus.html](https://www.sciaf.tauhwofer.de/snp-normalization-corpus.html)) & [68] \\ \hline Nested NER & & & \\ \hline GENIA & & [[https://github.com/openbiocorpora/genia-term](https://github.com/openbiocorpora/genia-term)]([https://github.com/openbiocorpora/genia-term](https://github.com/openbiocorpora/genia-term)) \({}^{*}\) & [69] \\ Bacteria biotopes & ✓ & [[https://sites.google.com/view/bb-2019/dataset?authuser=0](https://sites.google.com/view/bb-2019/dataset?authuser=0)]([https://sites.google.com/view/bb-2019/dataset?authuser=0](https://sites.google.com/view/bb-2019/dataset?authuser=0)) & [70] \\ \hline \hline \end{tabular} \({}^{*}\) Norm indicates NE normalization. \({}^{*}\) These URLs are not from official sources; they have been shared by independent users. URLs accessed on 14 December 2023.  
\end{table}