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NameTDescription# Ann. AuthorMaintainerUpdated_atStatus

561-580 / 593 show all
PubCasesORDO ORDO annotation in PubCases865 KToyofumi Fujiwara2023-11-24Beta
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
LitCovid-PD-HP 922 KJin-Dong Kim2023-11-28Beta
OryzaGP_2021 Updating OryzaGP1.08 MPierre Larmandelarmande2023-11-28Developing
NCBITAXON annotation for NCBI taxonomy. Automatic annotation by PD-NCBITaxon.1.1 MJin-Dong Kim2024-09-18Developing
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 Kim2023-11-29Released
mondo_disease annotation for diseases and disorders as defined in MONDO. Automatic annotation by PD-MONDO.1.16 MJin-Dong Kim2024-09-18Developing
LitCovid-PD-FMA-UBERON 1.3 MJin-Dong Kim2023-11-28Developing
Epistemic_Statements The goal of this work is to identify epistemic statements in the scientific literature. An epistemic statement is a statement of unknowns, hypotheses, speculations, uncertainties, including statements of claims, hypotheses, questions, explanations, future opportunities, surprises, issues, or concerns within a sentence. The unit of an epistemic statement is a sentence automatically parsed. The classification is binary - epistemic statement or not. We will label epistemic statements only and one can assume that if a statement is not labeled, then it is not an epistemic statement. The classifier is a CRF, trained on gold standard annotations of epistemic statements that are currently ongoing. We report an F-measure of 0.91 after 5-fold cross validation on a test set with 914 statements and an F-measure of 0.9 on a held out document with 130 statements. This project is still under development and is submitted to be used for the CovidLit project and associated Hackathon. Please contact Mayla if you have any questions.1.42 Mmboguslav2023-11-24Developing
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 Kim2023-11-24Released
LitCovid-PD-CHEBI 1.43 MJin-Dong Kim2023-11-24Developing
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
Anatomy-UBERON Anatomical structures based on UBERON.2.12 MJin-Dong Kim2024-09-19Developing
NEUROSES This corpus is composed of PubMed articles containing cognitive enhancers and anti-depressants drug mentions. The selected sentences are automatically annotated using the NCBO Annotator with the Chemical Entities of Biological Interest (CHEBI) and Phenotypic Quality Ontology (PATO) ontologies, we also produced annotations using PhenoMiner ontology via a dictionary-based tagger.2.14 Mnestoralvaro2023-11-24Beta
PMID_GLOBAL Global sentencer tagging of public PMID abstracts. Open and publicly available to the global community.2.24 Malo332023-11-24Developing
LitCovid-PD-MONDO 2.26 MJin-Dong Kim2023-11-24
DisGeNET Disease-Gene association annotation.3.12 MNuria Queralt Jin-Dong Kim2023-11-24Beta
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
PubCasesHPO HPO annotation in PubCases3.18 MToyofumi Fujiwara2023-11-24Beta
TEST0 3.37 MYue Wang2023-11-24
NameT# Ann. AuthorMaintainerUpdated_atStatus

561-580 / 593 show all
PubCasesORDO 865 KToyofumi Fujiwara2023-11-24Beta
Biotea 894 KL. Garcia2023-11-24Developing
LitCovid-PD-HP 922 KJin-Dong Kim2023-11-28Beta
OryzaGP_2021 1.08 MPierre Larmandelarmande2023-11-28Developing
NCBITAXON 1.1 MJin-Dong Kim2024-09-18Developing
CORD-19-PD-HP 1.15 MJin-Dong Kim2023-11-29Released
mondo_disease 1.16 MJin-Dong Kim2024-09-18Developing
LitCovid-PD-FMA-UBERON 1.3 MJin-Dong Kim2023-11-28Developing
Epistemic_Statements 1.42 Mmboguslav2023-11-24Developing
CORD-19-PD-UBERON 1.42 MJin-Dong Kim2023-11-24Released
LitCovid-PD-CHEBI 1.43 MJin-Dong Kim2023-11-24Developing
DisGeNET5_gene_disease 2.04 MIBI GroupYue Wang2023-11-24Released
Anatomy-UBERON 2.12 MJin-Dong Kim2024-09-19Developing
NEUROSES 2.14 Mnestoralvaro2023-11-24Beta
PMID_GLOBAL 2.24 Malo332023-11-24Developing
LitCovid-PD-MONDO 2.26 MJin-Dong Kim2023-11-24
DisGeNET 3.12 MNuria Queralt Jin-Dong Kim2023-11-24Beta
LitCovid-PMC-OGER-BB 3.14 MFabio RinaldiNico Colic2023-11-24Developing
PubCasesHPO 3.18 MToyofumi Fujiwara2023-11-24Beta
TEST0 3.37 MYue Wang2023-11-24