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NameTDescription# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 556 show all
NCBIDiseaseCorpus The NCBI disease corpus is fully annotated at the mention and concept level to serve as a research resource for the biomedical natural language processing community.6.85 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2023-11-29Released
LitCovid-OGER Using OGER (http://www.ontogene.org/resources/oger) to detect entities from 10 different vocabularies9.31 KFabio RinaldiNico Colic2023-11-29Released
RELISH-DB Abstracts contained in the data of the RELISH-DB (https://relishdb.ict.griffith.edu.au) made available for download here. Data was downloaded from here: https://figshare.com/projects/RELISH-DB/60095 Related publication: https://academic.oup.com/database/article/doi/10.1093/database/baz085/5608006#20072202302023-11-29Released
craft-ca-core-dev Development data for CRAFT CA shared task, core concepts only. This project contains the development (training) annotations for the Concept Annotation task of the CRAFT Shared Task 2019. This particular set of concept annotations is the "core" set. See the task description for details, but this set contains only annotations to concepts that appear in the original 10 Open Biomedical Ontologies used for annotation. (That is to say, it does not contain any annotations to extension classes).59.8 KUniversity of Colorado Anschutz Medical Campuscraft-st2023-11-29Released
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
bionlp-st-ge-2016-test It is the benchmark test data set of the BioNLP-ST 2016 GE task. It includes Genia-style event annotations to 14 full paper articles which are about NFκB proteins. For testing purpose, however, annotations are all blinded, which means users cannot see the annotations in this project. Instead, annotations in any other project can be compared to the hidden annotations in this project, then the annotations in the project will be automatically evaluated based on the comparison. A participant of GE task can get the evaluation of his/her result of automatic annotation, through following process: Create a new project. Import documents from the project, bionlp-st-2016-test-proteins to your project. Import annotations from the project, bionlp-st-2016-test-proteins to your project. At this point, you may want to compare you project to this project, the benchmark data set. It will show that protein annotations in your project is 100% correct, but other annotations, e.g., events, are 0%. Produce event annotations, using your system, upon the protein annotations. Upload your event annotations to your project. Compare your project to this project, to get evaluation. GE 2016 benchmark data set is provided as multi-layer annotations which include: bionlp-st-ge-2016-reference: benchmark reference data set bionlp-st-ge-2016-test: benchmark test data set (this project) bionlp-st-ge-2016-test-proteins: protein annotation to the benchmark test data set Following is supporting resources: bionlp-st-ge-2016-coref: coreference annotation bionlp-st-ge-2016-uniprot: Protein annotation with UniProt IDs. pmc-enju-pas: dependency parsing result produced by Enju UBERON-AE: annotation for anatomical entities as defined in UBERON ICD10: annotation for disease names as defined in ICD10 GO-BP: annotation for biological process names as defined in GO GO-CC: annotation for cellular component names as defined in GO A SPARQL-driven search interface is provided at http://bionlp.dbcls.jp/sparql.7.99 KDBCLSJin-Dong Kim2023-11-29Released
bionlp-st-ge-2016-reference-tees NER and event extraction produced by TEES (with the default GE11 model) for the 20 full papers used in the BioNLP 2016 GE task reference corpus.14.6 KNico Colic Nico Colic2023-11-29Released
CORD-19_bioRxiv_medRxiv_subset The bioRxiv/medRxiv subset of the CORD-19 dataset: pre-prints that are not peer reviewed. The documents in this project will be updated as the CORD-19 dataset grows. See the COVID DATASET LICENSE AGREEMENT. 0Jin-Dong Kim2023-11-29Released
CORD-19_Non-commercial_use_subset The Non commercial use 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.0Jin-Dong Kim2023-11-29Released
CORD-19_Commercial_use_subset The Commercial use 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.0Jin-Dong Kim2023-11-29Released
CORD-19_All_docs All the documents in the whole CORD-19 dataset. The documents in this project will be updated as the CORD-19 dataset grows. See the COVID DATASET LICENSE AGREEMENT.0Jin-Dong Kim2023-11-29Released
BioLarkPubmedHPO 228 abstracts manually annotated with Human Phenotype Ontology (HPO) concepts and harmonized by three curators, which can be used as a reference standard for free text annotation of human phenotypes. For more info, please see Groza et al. "Automatic concept recognition using the human phenotype ontology reference and test suite corpora", 2015.7.16 KTudor Grozasimon2023-11-29Released
AnEM_abstracts 250 documents selected randomly from citation abstracts Entity types: organism subdivision, anatomical system, organ, multi-tissue structure, tissue, cell, developing anatomical structure, cellular component, organism substance, immaterial anatomical entity and pathological formation Together with AnEM_full-texts, it is probably the largest manually annotated corpus on anatomical entities.1.91 KNaCTeMYue Wang2023-11-29Released
GENIAcorpus multi_cell (1,782) mono_cell (222) virus (2,136) protein_family_or_group (8,002) protein_complex (2,394) protein_molecule (21,290) protein_subunit (942) protein_substructure (129) protein_domain_or_region (1,044) protein_other (97) peptide (521) amino_acid_monomer (784) DNA_family_or_group (332) DNA_molecule (664) DNA_substructure (2) DNA_domain_or_region (39) DNA_other (16) RNA_family_or_group (1,545) RNA_molecule (554) RNA_substructure (106) RNA_domain_or_region (8,237) RNA_other (48) polynucleotide (259) nucleotide (243) lipid (2,375) carbohydrate (99) other_organic_compound (4,113) body_part (461) tissue (706) cell_type (7,473) cell_component (679) cell_line (4,129) other_artificial_source (211) inorganic (258) atom (342) other (21,056) 78.9 KGENIA ProjectYue Wang2023-11-29Released
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.0Jin-Dong Kim2023-11-29Released
LocText The manually annotated corpus consists of 100 PubMed abstracts annotated for proteins, subcellular localizations, organisms and relations between them. The focus of the corpus is on annotation of proteins and their subcellular localizations.2.29 KGoldberg et alShrikant Vinchurkar2023-11-29Released
LitCovid-v1-docs A comprehensive literature resource on the subject of Covid-19 is collected by NCBI: https://www.ncbi.nlm.nih.gov/research/coronavirus/ The LitCovid project@PubAnnotation is a collection of the titles and abstracts of the LitCovid dataset, for the people who want to perform text mining analysis. Please note that if you produce some annotation to the documents in this project, and contribute the annotation back to PubAnnotation, it will become publicly available together with contribution from other people. If you want to contribute your annotation to PubAnnotation, please refer to the documentation page: http://www.pubannotation.org/docs/submit-annotation/ The list of the PMID is sourced from here The 6 entries of the following PMIDs could not be included because they were not available from PubMed:32161394, 32104909, 32090470, 32076224, 32161394 32188956, 32238946. Below is a notice from the original LitCovid dataset: PUBLIC DOMAIN NOTICE National Center for Biotechnology Information This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose. Please cite the authors in any work or product based on this material : Chen Q, Allot A, & Lu Z. (2020) Keep up with the latest coronavirus research, Nature 579:193 0Jin-Dong Kim2023-11-29Released
LitCovid-docs-s 0Jin-Dong Kim2023-11-29Released
LitCovid-PD-MONDO-v1 PubDictionaries annotation for disease terms - updated at 2020-04-20 It is based on MONDO Version 2020-04-20. The terms in MONDO are loaded in PubDictionaries, with which the annotations in this project are produced. The parameter configuration used for this project is here. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.13.4 KJin-Dong Kim2023-11-29Released
LitCovid-PD-HP-v1 PubDictionaries annotation for human phenotype terms - updated at 2020-04-20 Disease term annotation based on HP. Version 2020-04-20. The terms in HP are loaded in PubDictionaries, with which the annotations in this project are produced. The parameter configuration used for this project is here. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.3.03 KJin-Dong Kim2023-11-29Released
NameT# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 556 show all
NCBIDiseaseCorpus 6.85 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2023-11-29Released
LitCovid-OGER 9.31 KFabio RinaldiNico Colic2023-11-29Released
RELISH-DB 02023-11-29Released
craft-ca-core-dev 59.8 KUniversity of Colorado Anschutz Medical Campuscraft-st2023-11-29Released
bionlp-st-ge-2016-test-tees 9.17 KNico ColicNico Colic2023-11-29Released
bionlp-st-ge-2016-test 7.99 KDBCLSJin-Dong Kim2023-11-29Released
bionlp-st-ge-2016-reference-tees 14.6 KNico Colic Nico Colic2023-11-29Released
CORD-19_bioRxiv_medRxiv_subset 0Jin-Dong Kim2023-11-29Released
CORD-19_Non-commercial_use_subset 0Jin-Dong Kim2023-11-29Released
CORD-19_Commercial_use_subset 0Jin-Dong Kim2023-11-29Released
CORD-19_All_docs 0Jin-Dong Kim2023-11-29Released
BioLarkPubmedHPO 7.16 KTudor Grozasimon2023-11-29Released
AnEM_abstracts 1.91 KNaCTeMYue Wang2023-11-29Released
GENIAcorpus 78.9 KGENIA ProjectYue Wang2023-11-29Released
GlyCosmos600-docs 0Jin-Dong Kim2023-11-29Released
LocText 2.29 KGoldberg et alShrikant Vinchurkar2023-11-29Released
LitCovid-v1-docs 0Jin-Dong Kim2023-11-29Released
LitCovid-docs-s 0Jin-Dong Kim2023-11-29Released
LitCovid-PD-MONDO-v1 13.4 KJin-Dong Kim2023-11-29Released
LitCovid-PD-HP-v1 3.03 KJin-Dong Kim2023-11-29Released