ENG_NER_NEL | | Annotations in COVID-19 related PubMed abstracts from the following ontologies: Disease Ontology ("do"), Gene Ontology ("go"), Human Phenotype Ontology ("hpo"), ChEBI ontology ("chebi"), MeSH
| 493 | LASIGE-DeST | pruas_18 | 2023-11-26 | Developing | |
PT_NER_NEL | | Annotations in Portuguese COVID-19 related abstracts from MeSH terminology | 245 | LASIGE-DeST | pruas_18 | 2023-11-29 | Developing | |
LitCoin-Disease-Tuning-1 | | Annotator=PD-MeSH2022_C_F03_plus_allFN-B | 6.98 K | | yucca | 2023-11-29 | | |
performance-test | | a project for performance test | 480 K | | Jin-Dong Kim | 2023-11-27 | Testing | |
GlyCosmos600-docs | | A random collection of 600 PubMed abstracts from 6 glycobiology-related journals: Glycobiology, Glycoconjugate journal, The Journal of biological chemistry, Journal of proteome research, Journal of proteomics, and Carbohydrate research. The whole PMIDs were collected on June 11, 2019. From each journal, 100 PMIDs were randomly sampled. | 0 | | Jin-Dong Kim | 2023-11-29 | Released | |
LitCovid-GlycoBiology | | Articles from GlycoBiology, received by the keyword "Covid-19" | 0 | | Jin-Dong Kim | 2023-11-29 | Testing | |
LitCoin-PubTator-for-Tuning | | A set of randomly selected PubMed articles with PubTator annotation.
The labels of PubTator annotations are converted to corresponding labels for LitCoin as follows:
'Gene' -> 'GeneOrGeneProduct',
'Disease' -> 'DiseaseOrPhenotypicFeature',
'Chemical' -> 'ChemicalEntity'
'Species' -> 'OrganismTaxon'
'Mutation' -> 'SequenceVariant'
'CellLine' -> 'CellLine' | 14.2 K | | Jin-Dong Kim | 2023-11-29 | | |
GlyCosmos6-Glycan-Motif-Structure | | Automatic annotation by Covid-19_Glycan-Motif. | 107 K | | Jin-Dong Kim | 2023-11-24 | Developing | |
GlyCosmos6-CLO | | Automatic annotation by PC-CLO. | 1.18 M | | Jin-Dong Kim | 2023-11-24 | Developing | |
Glycosmos6-GlycoEpitope | | Automatic annotation by PD-GlycoEpitope. | 19.9 K | | Jin-Dong Kim | 2023-11-28 | Developing | |
Glycosmos6-MAT | | Automatic annotation by PD-MAT. | 263 K | | Jin-Dong Kim | 2023-11-29 | Developing | |
CORD-PICO | | Automatic annotation of the CORD-19 dataset with PICO categories. The corpus was automatically labeled with an LSTM-CRF model trained on human-annotated PubMed abstracts from https://github.com/bepnye/EBM-NLP. Currently, titles and abstracts only are annotated using Population, Intervention and Outcome labels, as well as more fine-grained labels such as Age, Drug, Mortality and others. | 69.6 K | Simon Suster | ssuster | 2023-11-27 | Developing | |
LitCoin_CellLine | | CellLine | 113 | | Yasunori Yamamoto | 2023-11-29 | Developing | |
GlycoBiology-PACDB | | cGGDB-based annotation to GlycoBiology abstracts | 3.03 K | Toshihide Shikanai | shikanai | 2023-11-27 | Testing | |
GlycoBiology-cGGDB | | cGGDB-based annotation to GlycoBiology abstracts | 36 | Toshihide Shikanai | shikanai | 2023-11-28 | Testing | |
TEST-ChemicalEntity | | ChemicalEntity : Annotated by PD-MeSH2022_CHEBI_tuned-B | 827 | | yucca | 2023-11-29 | Beta | |
LitCoin-Chemical-MeSH-CHEBI | | ChemicalEntity:
Annotated by PD-MeSH2022_CHEBI_tuned-B | 3.84 K | | yucca | 2023-11-29 | Testing | |
UCDIT_TEST | | colitis link | 91.6 K | | alo33 | 2023-11-27 | Testing | |
BioASQ-sample | | collection of PubMed articles which appear in the BioASQ sample data set. | 0 | BioASQ | Jin-Dong Kim | 2023-11-28 | Testing | |
bionlp-st-ge-2016-spacy-parsed | | Dependency parses produced by spaCy parser, and part-of-speech tags produced by Stanford tagger (with the wsj-0-18-left3words-nodistsim model). The exact procedure is described here. Data set contains the 34 full paper articles used in the BioNLP 2016 GE task.
| 225 K | Nico Colic | Nico Colic | 2023-11-29 | Released | |