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Jin-Dong Kim
User info
Collections
NameDescription Updated at
11-12 / 12 show all
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
LitCovid-sampleVarious annotations to a sample set of LitCovid, to demonstrate potential of harmonized various annotations.2021-01-14
Projects
NameTDescription # Ann.Updated atStatus
111-120 / 161 show all
GlyCosmos600-docsA 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.02023-11-29Released
LitCovid-GlycoBiologyArticles from GlycoBiology, received by the keyword "Covid-19"02023-11-29Testing
DocumentLevelAnnotationSampleA sample project for document level annotation472023-11-29Testing
LitCoin-PubTator-for-TuningA set of randomly selected PubMed articles with PubTator annotation. The labels of PubTator annotations are converted to corresponding labels for LitCoin as follows: 'Gene' -> 'GeneOrGeneProduct', 'Disease' -> 'DiseaseOrPhenotypicFeature', 'Chemical' -> 'ChemicalEntity' 'Species' -> 'OrganismTaxon' 'Mutation' -> 'SequenceVariant' 'CellLine' -> 'CellLine'14.2 K2023-11-29
GlyCosmos6-Glycan-Motif-StructureAutomatic annotation by Covid-19_Glycan-Motif.107 K2023-11-24Developing
GlyCosmos6-CLOAutomatic annotation by PC-CLO.1.18 M2023-11-24Developing
Glycosmos6-GlycoEpitopeAutomatic annotation by PD-GlycoEpitope.19.9 K2023-11-28Developing
Glycosmos6-MATAutomatic annotation by PD-MAT.263 K2023-11-29Developing
BioASQ-samplecollection of PubMed articles which appear in the BioASQ sample data set.02023-11-28Testing
genia-medco-corefCoreference annotation made to the Genia corpus, following the MUC annotation scheme. It is a product of the collaboration between the Genia and the MedCo projects.45.9 K2023-11-24Developing
Automatic annotators
NameDescription
11-20 / 39 show all
PD-FMA-PAEPhysical Anatomical Entities from FMA
PD-UBERON-AEIt annotates for anatomical entities, based on the UBERON-AE dictionary on PubDictionaries. Threshold is set to 0.85.
PD-UBERON-AE-BIt annotates for anatomical entities, based on the UBERON-AE dictionary on PubDictionaries. It used the default threshold, 0.85. It uses the batch mode annotation, and may be used for annotation to a large amount of documents.
PD-UBERON-AE-2023It annotates for anatomical entities, based on the UBERON-AE-2023 dictionary on PubDictionaries. Threshold is set to 0.85.
EnjuParserEnju HPSG Parser developed by University of Tokyo.
PD-GO-BP-BBiological Processes as defined in GO
PD-FMA-PAE-BBatch mode annotator of PD-FMA-PAE
discourse-simplifierA discourse analyzer developed by Univ. Manchester.
PD-GlycoEpitope-BA batch annotator using PubDictionaries with the dictionary 'GlycoEpitope'
PD-NGLY1-deficiency-BA batch annotator for NGLY1 deficiency
Editors
NameDescription
1-2 / 2
TextAETextAE version 5, which enables edition of attributes of denotations.
TextAE-oldTextAE version 4, which was the latest stable version until Apr. 19, 2020.