| SPECIES800 | | SPECIES 800 (S800): an abstract-based manually annotated corpus. S800 comprises 800 PubMed abstracts in which organism mentions were identified and mapped to the corresponding NCBI Taxonomy identifiers.
Described in:
The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text.
Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, et al. (2013). PLoS ONE, 2013, 8(6): e65390. doi:10.1371/journal.pone.0065390 | 3.71 K | Evangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensen | evangelos | 2023-11-28 | Released | |
| 2015-BEL-Sample-2 | | The 295 BEL statements for sample set used for the 2015 BioCreative challenge. | 11.4 K | Fabio Rinaldi | Nico Colic | 2023-11-28 | Released | |
| 2015-BEL-Sample | | An attempt to upload 295 BEL statements, i.e. the sample set used for the 2015 BioCreative challenge.
| 58 | Fabio Rinaldi | Fabio Rinaldi | 2023-11-29 | Testing | |
| bionlp-st-epi-2011-training | | The training dataset from the Epigenetics and Post-translational Modifications (EPI) task in the BioNLP Shared Task 2011.
The core entities of the task are genes and gene products (RNA and proteins), identified in the data simply as "Protein" annotations. | 7.59 K | GENIA | Yue Wang | 2023-11-29 | Released | |
| jnlpba-st-training | | The training data used in the task came from the GENIA version 3.02 corpus, This was formed from a controlled search on MEDLINE using the MeSH terms "human", "blood cells" and "transcription factors". From this search, 1,999 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus. For the shared task only the classes protein, DNA, RNA, cell line and cell type were used. The first three incorporate several subclasses from the original taxonomy while the last two are interesting in order to make the task realistic for post-processing by a potential template filling application. The publication year of the training set ranges over 1990~1999. | 51.1 K | GENIA | Yue Wang | 2023-11-26 | Released | |
| pubmed-sentences-benchmark | | A benchmark data for text segmentation into sentences.
The source of annotation is the GENIA treebank v1.0.
Following is the process taken.
began with the GENIA treebank v1.0.
sentence annotations were extracted and converted to PubAnnotation JSON.
uploaded. 12 abstracts met alignment failure.
among the 12 failure cases, 4 had a dot('.') character where there should be colon (':'). They were manually fixed then successfully uploaded: 7903907, 8053950, 8508358, 9415639.
among the 12 failed abstracts, 8 were "250 word truncation" cases. They were manually fixed and successfully uploaded. During the fixing, manual annotations were added for the missing pieces of text.
30 abstracts had extra text in the end, indicating copyright statement, e.g., "Copyright 1998 Academic Press." They were annotated as a sentence in GTB. However, the text did not exist anymore in PubMed. Therefore, the extra texts were removed, together with the sentence annotation to them.
| 18.4 K | GENIA project | Jin-Dong Kim | 2023-11-28 | Released | |
| GENIAcorpus | | multi_cell (1,782)
mono_cell (222)
virus (2,136)
protein_family_or_group (8,002)
protein_complex (2,394)
protein_molecule (21,290)
protein_subunit (942)
protein_substructure (129)
protein_domain_or_region (1,044)
protein_other (97)
peptide (521)
amino_acid_monomer (784)
DNA_family_or_group (332)
DNA_molecule (664)
DNA_substructure (2)
DNA_domain_or_region (39)
DNA_other (16)
RNA_family_or_group (1,545)
RNA_molecule (554)
RNA_substructure (106)
RNA_domain_or_region (8,237)
RNA_other (48)
polynucleotide (259)
nucleotide (243)
lipid (2,375)
carbohydrate (99)
other_organic_compound (4,113)
body_part (461)
tissue (706)
cell_type (7,473)
cell_component (679)
cell_line (4,129)
other_artificial_source (211)
inorganic (258)
atom (342)
other (21,056)
| 78.9 K | GENIA Project | Yue Wang | 2023-11-29 | Released | |
| LocText | | The manually annotated corpus consists of 100 PubMed abstracts annotated for proteins, subcellular localizations, organisms and relations between them. The focus of the corpus is on annotation of proteins and their subcellular localizations. | 2.29 K | Goldberg et al | Shrikant Vinchurkar | 2023-11-29 | Released | |
| hahm_test | | hahm_test | 0 | hahm | kaist_nlp | 2019-04-02 | Testing | |
| Tester | | Test for cancer | 93 | Han | | 2023-11-30 | Testing | |
| Staphylococcus | | | 7.46 K | haruo | haruo | 2023-11-29 | Testing | |
| CoGe_Citation_Annotations | | Annotated PMC abstracts+full articles, that cite the "CoGe" papers (PMID: 18952863, 18269575).
Total Num Citations: 165
Total Num Unique Citations: 141
Total Num Abstracts: 165
Total Num Whole Articles: 165 | 0 | Heather Lent | hclent | 2023-11-29 | Uploading | |
| test1 | | test1 | 21 | H. S. Park | Sophie Nam | 2023-11-26 | Testing | |
| Virus300 | | 300 abstracts from virology journals annotated with viral proteins and species | 0 | http://aclweb.org/anthology/W/W17/W17-2311.pdf | helencook | 2017-08-07 | Released | |
| OryzaGP1 | | A dataset for Named Entity Recognition for rice gene | 0 | Huy Do. Pierre Larmande | | 2019-01-31 | Uploading | |
| Genomics_Informatics | | Genomics & Informatics (NLM title abbreviation: Genomics Inform) is the official journal of the Korea Genome Organization.
Text corpus for this journal annotated with various levels of linguistic information would be a valuable resource as the process of information extraction requires syntactic, semantic, and higher levels of natural language processing. In this study, we publish our new corpus called GNI Corpus version 1.0, extracted and annotated from full texts of Genomics & Informatics, with NLTK (Natural Language ToolKit)-based text mining script. The preliminary version of the corpus could be used as a training and testing set of a system that serves a variety of functions for future biomedical text mining. | 35.3 K | Hyun-Seok Park | ewha-bio | 2023-11-29 | Beta | |
| Testing | | Testing | 241 | Hyun-Seok Park | hsp20 | 2023-11-28 | Testing | |
| falsetest_150825 | | test | 0 | ichihara_hisako | Hisako Ichihara | 2015-09-11 | Testing | |
| ichiharatest_150825_3 | | test | 0 | ichihara_hisako | Hisako Ichihara | 2023-11-26 | Testing | |
| ichiharatest_150825 | | test | 0 | ichihara_hisako | Hisako Ichihara | 2023-11-29 | Testing | |
