| 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 | 2023-11-26 | Released | |
| bionlp-st-pc-2013-training | | The training dataset from the pathway curation (PC) task in the BioNLP Shared Task 2013.
The entity types defined in the PC task are simple chemical, gene or gene product, complex and cellular component. | 7.86 K | 2023-11-27 | Released | |
| bionlp-st-id-2011-training | | The training dataset from the infectious diseases (ID) task in the BioNLP Shared Task 2011.
Entity types: - Genes and gene products: gene, RNA, and protein name mentions. - Two-component systems: mentions of the names of two-component regulatory systems, frequently embedding the names of the two Proteins forming the system.- Chemicals: mentions of chemical compounds such as "NaCL".- Organisms: mentions of organism names or organism specification through specific properties (e.g. "graRS mutant").- Regulons/Operons: mentions of names of specific regulons and operons. | 5.61 K | 2023-11-28 | Released | |
| 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 | 2023-11-29 | Released | |
| bionlp-st-cg-2013-training | | The training dataset from the cancer genetics task in the BioNLP Shared Task 2013.
Composed of anatomical and molecular entities. | 10.9 K | 2023-11-28 | Released | |
| PIR-corpus2 | | The protein tag was used to tag proteins, or protein-associated or -related objects, such as domains, pathways, expression of gene.
Annotation guideline: http://pir.georgetown.edu/pirwww/about/doc/manietal.pdf | 5.52 K | 2023-11-29 | Released | |
| PIR-corpus1 | | The Protein Information Resource (PIR) is not biased towards any particular biomedical domain, and is expected to provide more diverse protein names in a given sample size.
Annotation category: protein, compound-protein, acronym. | 4.44 K | 2023-11-27 | Released | |
| PennBioIE | | The PennBioIE corpus (0.9) covers two domains of biomedical knowledge. One is the inhibition of the cytochrome P450 family of enzymes (CYP450 or CYP for short) , and the other domain is the molecular genetics of dance (oncology or onco for short). | 23.8 K | 2023-11-26 | Released | |
| DisGeNET5_variant_disease | | The file contains variant-disease associations obtained by text mining MEDLINE abstracts using the BeFree system, including the variant and disease off sets. | 144 K | 2023-11-24 | Released | |
| DisGeNET5_gene_disease | | The file contains gene-disease associations obtained by text mining MEDLINE abstracts using the BeFree system including the gene and disease off sets. | 2.04 M | 2023-11-24 | Released | |
