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NameTDescription# Ann.Author MaintainerUpdated_atStatus

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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
LitCovid-OGER Using OGER (http://www.ontogene.org/resources/oger) to detect entities from 10 different vocabularies9.31 KFabio RinaldiNico Colic2023-11-29Released
LitCovid-OGER-BB Using OGER (www.ontogene.com) and Biobert to obtain annotations for 10 different vocabularies.308 KFabio RinaldiNico Colic2023-11-28Released
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
OryzaGP A dataset for Named Entity Recognition for rice gene29.1 KHuy Do and Pierre LarmandeYue Wang2023-11-24Uploading
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 KIBI GroupYue Wang2023-11-24Released
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 MIBI GroupYue Wang2023-11-24Released
AGCA_Sue Active Gene Annotation Corpus for the Application in Drug Repurposing Discovery0Jingbo Xia, Xuan Qin, Kaiyin Zhou2023-11-29Developing
causal0001 test0ju-hyuck hanJu-Hyuck Han2024-01-17
LappsTest Project to test posting annotations directly from the Language Applications Grid2.67 KKeith Sudermanksuderman2023-11-27Developing
KYMEKA20240117Test This is a project to express the linking of terms and ontologies (DOID, FMA, Radlex) used in the dataset 'Annotationdata_type-2' used in BLAH8_Radiological Causal Annotation.0Kyung-Min ChaeKyung-Min Chae2024-01-17Testing
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 493LASIGE-DeSTpruas_182023-11-26Developing
PT_NER_NEL Annotations in Portuguese COVID-19 related abstracts from MeSH terminology245LASIGE-DeSTpruas_182023-11-29Developing
Biotea NCBO annotation on full text for PMC articles. Currently including only a small set of 2811 articles corresponding to those supporting curated diesease-protein annotation from UniProt and with machine-processable full text.894 KL. Garcia2023-11-24Developing
bionlp-st-ge-2016-test-ihmc 14.4 KLucian Galescu2023-11-29Testing
biosemtest test submitting Peregrine annotations35.6 KMark Thompsonmarkthompson2023-11-29Testing
BLAH2015_Annotations_Adderall 0nestoralvaronestoralvaro2023-11-29Testing
spacy-test Random set of articles used for testing in the development of the RESTful spaCy parsing web service. Since development is now finished, they are released for the community to use.131 KNico ColicNico Colic2023-11-29Released
bionlp-st-ge-2016-test-tees NER and event extraction produced by TEES (with the default GE11 model) for the 14 full papers used in the BioNLP 2016 GE task test corpus.9.17 KNico ColicNico Colic2023-11-29Released
tees-test Random PMC document used for testing during the development of a RESTful TEES parsing web service.3.39 KNico ColicNico Colic2023-11-24Developing
NameT# Ann.Author MaintainerUpdated_atStatus

201-220 / 238 show all
SPECIES800_autotagged 0Evangelos Pafilis, Sampo Pyysalo, Lars Juhl Jensenevangelos2015-11-20Testing
LitCovid-OGER 9.31 KFabio RinaldiNico Colic2023-11-29Released
LitCovid-OGER-BB 308 KFabio RinaldiNico Colic2023-11-28Released
LitCovid-PMC-OGER-BB 3.14 MFabio RinaldiNico Colic2023-11-24Developing
OryzaGP 29.1 KHuy Do and Pierre LarmandeYue Wang2023-11-24Uploading
DisGeNET5_variant_disease 144 KIBI GroupYue Wang2023-11-24Released
DisGeNET5_gene_disease 2.04 MIBI GroupYue Wang2023-11-24Released
AGCA_Sue 0Jingbo Xia, Xuan Qin, Kaiyin Zhou2023-11-29Developing
causal0001 0ju-hyuck hanJu-Hyuck Han2024-01-17
LappsTest 2.67 KKeith Sudermanksuderman2023-11-27Developing
KYMEKA20240117Test 0Kyung-Min ChaeKyung-Min Chae2024-01-17Testing
ENG_NER_NEL 493LASIGE-DeSTpruas_182023-11-26Developing
PT_NER_NEL 245LASIGE-DeSTpruas_182023-11-29Developing
Biotea 894 KL. Garcia2023-11-24Developing
bionlp-st-ge-2016-test-ihmc 14.4 KLucian Galescu2023-11-29Testing
biosemtest 35.6 KMark Thompsonmarkthompson2023-11-29Testing
BLAH2015_Annotations_Adderall 0nestoralvaronestoralvaro2023-11-29Testing
spacy-test 131 KNico ColicNico Colic2023-11-29Released
bionlp-st-ge-2016-test-tees 9.17 KNico ColicNico Colic2023-11-29Released
tees-test 3.39 KNico ColicNico Colic2023-11-24Developing