| PubCasesCollection | | abstracts in PubCases | 0 | | Jin-Dong Kim | 2023-11-29 | | |
| AlvisNLP-Async-Test | | Test for the asynchronous AlvisNLP/ML annotator family. | 0 | Robert Bossy | rbossy | 2023-11-26 | Testing | |
| IU_X-Ray_Round1_y | | | 0 | | Yuka Tateisi | 2025-12-02 | | |
| PubMed-2000 | | abstracts published in 2000. | 0 | | Jin-Dong Kim | 2023-11-29 | Developing | |
| GlycoConjugate-collection | | The PubMed entries (titles and abstracts) from the journal of GlycoConjugate | 0 | | Jin-Dong Kim | 2023-11-28 | Developing | |
| Molecular_Biology | | | 0 | | Sophie Nam | 2023-11-29 | | |
| 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 | |
| pubmed-2016 | | abstracts published in 2016 | 0 | | Jin-Dong Kim | 2023-11-28 | | |
| example-dialog | | | 0 | | Jin-Dong Kim | 2023-11-27 | Testing | |
| AGCA_Sue | | Active Gene Annotation Corpus for the Application in Drug Repurposing Discovery | 0 | Jingbo Xia, Xuan Qin, Kaiyin Zhou | | 2023-11-29 | Developing | |
| 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 | |
| GlycoBiology-GO | | GO-based annotation to GlycoBiology abstracts | 0 | | Jin-Dong Kim | 2023-11-29 | Testing | |
| IMDB-NLP | | Annotations for chunking and semantic role labeling based on in-memory databases. | 0 | | | 2016-05-06 | Uploading | |
| bc2gn_test | | test | 0 | | | 2021-07-13 | Testing | |
| BioASQ-sample | | collection of PubMed articles which appear in the BioASQ sample data set. | 0 | BioASQ | Jin-Dong Kim | 2023-11-28 | Testing | |
| IU_X-Ray_Round1 | | | 0 | | kenkim2 | 2025-12-02 | | |
| GlyCosmos600-GlycoGene3 | | | 0 | | angata | 2023-11-29 | Testing | |
| test_disfluency_annotation_auto_jp | | | 0 | | Jin-Dong Kim | 2023-12-28 | Testing | |
| BLAH2015_Annotations_Adderall | | | 0 | nestoralvaro | nestoralvaro | 2023-11-29 | Testing | |
| SMAFIRA_Methods | | Predictions for methods for the SMAFIRA project. | 0 | | zebet | 2023-11-28 | Developing | |
