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Jin-Dong Kim
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Collections
Name DescriptionUpdated at
1-10 / 12 show all
bionlp-st-ge-2016The 2016 edition of the Genia event extraction (GE) task organized within BioNLP-ST 20162019-03-11
CORD-19CORD-19 (COVID-19 Open Research Dataset) is a free, open resource for the global research community provided by the Allen Institute for AI: https://pages.semanticscholar.org/coronavirus-research. As of 2020-03-20, it contains over 29,000 full text articles. This CORD-19 collection at PubAnnotation is prepared for the purpose of collecting annotations to the texts, so that they can be easily accessed and utilized. If you want to contribute with your annotation, take the documents in the CORD-19_All_docs project, produce your annotation to the texts using your annotation system, and contribute the annotation back to PubAnnotation (HowTo). All the contributed annotations will become publicly available. Please note that, during uploading your annotation data, you do not need to be worried about slight changes in the text: PubAnnotation will automatically catch them and adjust the positions appropriately. Once you have uploaded your annotation, please notify it to admin@pubannotation.org admin@pubannotation.org, so that it can be included in this collection, which will make your annotation much easily findable. Note that as the CORD-19 dataset grows, the documents in this collection also will be updated. IMPORTANT: CORD-19 License agreement requires that the dataset must be used for text and data mining only.2020-04-14
CORD-19-sample-annotation2020-04-21
GlycoBiologyAnnotations made to the titles and abstracts of the journal 'GlycoBiology'2019-03-10
GlyCosmos15Collection of annotations to the abstracts from the following journals: Analytical_Chemistry Biochim_Biophys_Acta Carbohydrate_Research Cell Glycobiology Glycoconjugate_Journal J_Am_Chem_Soc Journal_of_Biological_Chemistry Journal_of_Proteome_Research Journal_of_Proteomics Molecular_and_Cellular_Proteomics Nature_Biotechnology Nature_Communications Nature_Methods Scientific_Reports 2024-09-19
Glycosmos6This collection contains annotation projects which target all the PubMed abstracts (at the time of January 14, 2022) from the 6 glycobiology-related journals: Glycobiology Glycoconjugate journal The Journal of biological chemistry Journal of proteome research Journal of proteomics Carbohydrate research 2023-11-16
GlyCosmos600A 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.2021-10-22
LitCoin2021-12-14
LitCovid2021-10-18
LitCovid-sampleVarious annotations to a sample set of LitCovid, to demonstrate potential of harmonized various annotations.2021-01-14
Projects
NameTDescription# Ann.Updated atStatus
1-10 / 163 show all
BioASQ-samplecollection of PubMed articles which appear in the BioASQ sample data set.02023-11-28Testing
CHEMDNER-training-testThe training subset of the CHEMDNER corpus29.4 K2023-11-27Testing
pubtator-sampleSample annotation of PubTator produced by Zhiyong Lu et al.282023-11-27Testing
LitCovid-sample-PD-MAT2512023-11-29Developing
GlycoBiology-FMAFMA ontology-based annotation to GlycoBiology abstracts96.3 K2023-11-29Testing
metamap-sampleSample annotation of MetaMep, produced by Aronson, et al. An overview of MetaMap: historical perspective and recent advances, JAMIA 201010.9 K2023-11-27Testing
uniprot-mouseProtein annotation based on UniProt11.5 K2023-11-28Developing
LitCovid-sample-Glycan3.21 K2023-11-29Testing
LitCoin-training-merged14.8 K2023-11-24
EDAM-topicsannotation for EDAM topics11.6 K2023-11-29Testing
Automatic annotators
Name Description
1-10 / 38 show all
discourse-simplifierA discourse analyzer developed by Univ. Manchester.
EnjuParserEnju HPSG Parser developed by University of Tokyo.
Glycan-GlyCosmos
Glycan-Image
Glycan-Motif-Image
PD-CHEBIPubdictionaries annotation using the terms sourced from CHEBI, the 2020-03-31 version
PD-CHEBI-B
PD-CLO
PD-CLO-B
PD-FMA-PAEPhysical Anatomical Entities from FMA
Editors
NameDescription
1-1 / 1
TextAEThe official stable version of TextAE.