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NameTDescription# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 381 show all
LitCovid-OGER-BB Using OGER (www.ontogene.com) and Biobert to obtain annotations for 10 different vocabularies.223 KFabio RinaldiNico Colic2020-06-04Released
LitCovid-PD-HP 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.3.02 KJin-Dong Kim2020-05-25Released
CORD-19-PD-HP PubDictionaries annotation for HP terms - updated at 2020-04-30 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.1.15 MJin-Dong Kim2020-05-12Released
LitCovid-PD-MONDO 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 Kim2020-05-10Released
LitCovid-PD-FMA-UBERON PubDictionaries annotation for anatomy terms - updated at 2020-04-20 Disease term annotation based on FMA and Uberon. Version 2020-04-20. The terms in FMA and Uberon are loaded in PubDictionaries (FMA and Uberon), with which the annotations in this project are produced. The parameter configuration used for this project is here for FMA and there for Uberon. 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.4.29 KJin-Dong Kim2020-05-10Released
CORD-19-PD-UBERON PubDictionaries annotation for UBERON terms - updated at 2020-04-30 It is disease term annotation based on Uberon. The terms in Uberon are uploaded in PubDictionaries (Uberon), 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.1.42 MJin-Dong Kim2020-04-30Released
CORD-19-PD-MONDO PubDictionaries annotation for MONDO terms - updated at 2020-04-30 It is disease term annotation 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.6.32 MJin-Dong Kim2020-04-30Released
LitCovid-PubTator 22.6 KJin-Dong Kim2020-04-21Released
LitCovid-sentences Sentence segmentation of all the texts in the LitCovid literature. The segmentation is automatically obtained using the TextSentencer annotation service developed and maintained by DBCLS.16.5 KJin-Dong Kim2020-04-14Released
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 Kim2020-04-10Released
LitCovid-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 Kim2020-04-08Released
LitCovid-OGER-BioBert Using OGER (http://www.ontogene.org/resources/oger) in conjunction with BioBert as described here (https://arxiv.org/pdf/2003.07424.pdf)4.03 KFabio RinaldiNico Colic2020-04-02Released
LitCovid-OGER Using OGER (http://www.ontogene.org/resources/oger) to detect entities from 10 different vocabularies9.31 KFabio RinaldiNico Colic2020-04-02Released
LitCovid-PubTatorCentral Named-entities for the documents in the LitCovid dataset. Annotations were automatically predicted by the PubTatorCentral tool (https://www.ncbi.nlm.nih.gov/research/pubtator/)4.64 Kzebet2020-04-01Released
PubMed_ArguminSci Predictions for PubMed automatically extracted with the ArguminSci tool (https://github.com/anlausch/ArguminSci).766 Kzebet2020-03-31Released
PubMed_Structured_Abstracts Sections (zones) as retrieved from PubMed.129 Kzebet2020-03-31Released
LitCovid-ArguminSci Discourse elements for the documents in the LitCovid dataset. Annotations were automatically predicted by the ArguminSci tool (https://github.com/anlausch/ArguminSci)4.9 Kzebet2020-03-25Released
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 Kim2020-03-23Released
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 Kim2020-03-23Released
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 Kim2020-03-23Released
NameT# Ann.AuthorMaintainerUpdated_atStatus

1-20 / 381 show all
LitCovid-OGER-BB 223 KFabio RinaldiNico Colic2020-06-04Released
LitCovid-PD-HP 3.02 KJin-Dong Kim2020-05-25Released
CORD-19-PD-HP 1.15 MJin-Dong Kim2020-05-12Released
LitCovid-PD-MONDO 13.4 KJin-Dong Kim2020-05-10Released
LitCovid-PD-FMA-UBERON 4.29 KJin-Dong Kim2020-05-10Released
CORD-19-PD-UBERON 1.42 MJin-Dong Kim2020-04-30Released
CORD-19-PD-MONDO 6.32 MJin-Dong Kim2020-04-30Released
LitCovid-PubTator 22.6 KJin-Dong Kim2020-04-21Released
LitCovid-sentences 16.5 KJin-Dong Kim2020-04-14Released
CORD-19_Custom_license_subset 5.08 MJin-Dong Kim2020-04-10Released
LitCovid-docs 0Jin-Dong Kim2020-04-08Released
LitCovid-OGER-BioBert 4.03 KFabio RinaldiNico Colic2020-04-02Released
LitCovid-OGER 9.31 KFabio RinaldiNico Colic2020-04-02Released
LitCovid-PubTatorCentral 4.64 Kzebet2020-04-01Released
PubMed_ArguminSci 766 Kzebet2020-03-31Released
PubMed_Structured_Abstracts 129 Kzebet2020-03-31Released
LitCovid-ArguminSci 4.9 Kzebet2020-03-25Released
CORD-19_Non-commercial_use_subset 0Jin-Dong Kim2020-03-23Released
CORD-19_Commercial_use_subset 0Jin-Dong Kim2020-03-23Released
CORD-19_bioRxiv_medRxiv_subset 0Jin-Dong Kim2020-03-23Released