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NameTDescription# Ann.AuthorMaintainerUpdated_at Status

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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). 0Evangelos Pafilis, Sampo Pyysalo, Lars Juhl Jensenevangelos2015-11-20Testing
IMDB-NLP Annotations for chunking and semantic role labeling based on in-memory databases.02016-05-06Uploading
bc2gn_test test02021-07-13Testing
Text-Annotation 02022-01-17
geneset_names 0alo332022-04-26Released
2_test 145 MYue Wang2023-11-24
Inflammaging Inflammation axis23.4 Malo332023-11-24Released
pubmed-enju-pas Annotating PubMed abstracts for predicate-argument structure (PAS). Enju 2.4.2 is used to automatically compute PAS.19.1 MEnjuJin-Dong Kim2023-11-24Developing
CORD-19-Sentences 13.4 MJin-Dong Kim2023-11-24Testing
PubmedHPO Human phenotype annotation to PubMed abstracts, based on the HPO ontology12.4 MTudor Grozatudor2023-11-24Beta
Allie An annotation set of abbreviations and expanded forms extracted from PubMed/MEDLINE by machines.8.7 MDatabase Center for Life ScienceYasunori Yamamoto2023-11-24Developing
LitCovid-PubTator 5.88 MJin-Dong Kim2023-11-24Beta
LitCovid-sentences 5.63 MJin-Dong Kim2023-11-24Developing
CORD-19_Custom_license_subset The Custom license subset of the CORD-19 dataset. The documents in this project will be updated as the CORD-19 dataset grows. See the COVID DATASET LICENSE AGREEMENT.5.08 MJin-Dong Kim2023-11-24Released
LitCovid-PD-CLO 3.73 MJin-Dong Kim2023-11-24Developing
TEST0 3.37 MYue Wang2023-11-24
PubCasesHPO HPO annotation in PubCases3.18 MToyofumi Fujiwara2023-11-24Beta
LitCovid-PMC-OGER-BB Annotating PMC articles with OGER and BioBert, according to an hand-crafted Covid-specific dictionary and the 10 different CRAFT ontologies (http://bionlp-corpora.sourceforge.net/CRAFT/): Chemical Entities of Biological Interest (CHEBI), Cell Ontology (CL), Entrez Gene (UBERON), Gene Ontology (biological process (GO-BP), cellular component (GO-CC), and molecular function (GO-MF), NCBI Taxonomy (NCBITaxon), Protein Ontology (PR), Sequence Ontology (SO)3.14 MFabio RinaldiNico Colic2023-11-24Developing
DisGeNET Disease-Gene association annotation.3.12 MNuria Queralt Jin-Dong Kim2023-11-24Beta
PMID_GLOBAL Global sentencer tagging of public PMID abstracts. Open and publicly available to the global community.2.24 Malo332023-11-24Developing
NameT# Ann.AuthorMaintainerUpdated_at Status

1-20 / 338 show all
SPECIES800_autotagged 0Evangelos Pafilis, Sampo Pyysalo, Lars Juhl Jensenevangelos2015-11-20Testing
IMDB-NLP 02016-05-06Uploading
bc2gn_test 02021-07-13Testing
Text-Annotation 02022-01-17
geneset_names 0alo332022-04-26Released
2_test 145 MYue Wang2023-11-24
Inflammaging 23.4 Malo332023-11-24Released
pubmed-enju-pas 19.1 MEnjuJin-Dong Kim2023-11-24Developing
CORD-19-Sentences 13.4 MJin-Dong Kim2023-11-24Testing
PubmedHPO 12.4 MTudor Grozatudor2023-11-24Beta
Allie 8.7 MDatabase Center for Life ScienceYasunori Yamamoto2023-11-24Developing
LitCovid-PubTator 5.88 MJin-Dong Kim2023-11-24Beta
LitCovid-sentences 5.63 MJin-Dong Kim2023-11-24Developing
CORD-19_Custom_license_subset 5.08 MJin-Dong Kim2023-11-24Released
LitCovid-PD-CLO 3.73 MJin-Dong Kim2023-11-24Developing
TEST0 3.37 MYue Wang2023-11-24
PubCasesHPO 3.18 MToyofumi Fujiwara2023-11-24Beta
LitCovid-PMC-OGER-BB 3.14 MFabio RinaldiNico Colic2023-11-24Developing
DisGeNET 3.12 MNuria Queralt Jin-Dong Kim2023-11-24Beta
PMID_GLOBAL 2.24 Malo332023-11-24Developing