| 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 | IBI Group | Yue Wang | 2023-11-24 | Released | |
| OryzaGP | | A dataset for Named Entity Recognition for rice gene | 29.1 K | Huy Do and Pierre Larmande | Yue Wang | 2023-11-24 | Uploading | |
| Parkinson | | | 54 | | Jin-Dong Kim | 2023-11-28 | Testing | |
| GlyCosmos600-GlycoGenes | | | 87 | | Jin-Dong Kim | 2023-11-28 | Testing | |
| GlycoBiology-Motifs | | | 4.15 K | | Jin-Dong Kim | 2023-11-29 | | |
| SPECIES800_autotagged | | This project comprises the SPECIES800 corpus documents automatically annotated by the Jensenlab tagger.
Annotated entity types are:
Genes/proteins from the mentioned organisms (and any human ones)
PubChem Compound identifiers
NCBI Taxonomy entries
Gene Ontology cellular component terms
BRENDA Tissue Ontology terms
Disease Ontology terms
Environment Ontology terms
The SPECIES 800 (S800) comprises 800 PubMed abstracts. In its original form species mentions were manually 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.
The manually annotated corpus is also available as a PubAnnotation project (see here).
| 0 | Evangelos Pafilis, Sampo Pyysalo, Lars Juhl Jensen | evangelos | 2015-11-20 | Testing | |
| PubCasesCollection | | abstracts in PubCases | 0 | | Jin-Dong Kim | 2023-11-29 | | |
| SMAFIRA_Methods | | Predictions for methods for the SMAFIRA project. | 0 | | zebet | 2023-11-28 | Developing | |
| LitCovid-docs-s | | | 0 | | Jin-Dong Kim | 2023-11-29 | Released | |
| LitCoin-training-merged | | | 14.8 K | | Jin-Dong Kim | 2023-11-24 | | |
| GlycoBiology-PACDB | | cGGDB-based annotation to GlycoBiology abstracts | 3.03 K | Toshihide Shikanai | shikanai | 2023-11-27 | Testing | |
| Grays_part1_test | | | 0 | | Jin-Dong Kim | 2023-11-29 | Testing | |
| EDAM-topics | | annotation for EDAM topics | 11.6 K | | Jin-Dong Kim | 2023-11-29 | Testing | |
| LitCoin-Disease-Tuning-1 | | Annotator=PD-MeSH2022_C_F03_plus_allFN-B | 6.98 K | | yucca | 2023-11-29 | | |
| LitCoin-PubTator_CellLine | | | 388 | | Yasunori Yamamoto | 2023-11-29 | Testing | |
| excludesZoonoses | | | 25 | | AikoHIRAKI | 2023-11-29 | Developing | |
| EDAM-DFO | | annotation for EDAM terms for data, formats, and operations | 12.5 K | | Jin-Dong Kim | 2023-11-29 | Testing | |
| GlycoBiology-cGGDB | | cGGDB-based annotation to GlycoBiology abstracts | 36 | Toshihide Shikanai | shikanai | 2023-11-28 | Testing | |
| pubtator-sample | | Sample annotation of PubTator produced by Zhiyong Lu et al. | 28 | Zhiyong Lu | Jin-Dong Kim | 2023-11-27 | Testing | |
| Text-Annotation | | | 0 | | | 2022-01-17 | | |
