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Jin-Dong Kim
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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
101-110 / 159 show all
ICD10Annotation for disease names as defined in ICD101.6 K2023-11-29Developing
mondo_diseaseannotation for diseases and disorders as defined in MONDO. Automatic annotation by PD-MONDO.256 K2023-11-28Developing
EDAM-DFOannotation for EDAM terms for data, formats, and operations12.5 K2023-11-29Testing
EDAM-topicsannotation for EDAM topics11.6 K2023-11-29Testing
GlycoGenesannotation for glyco-genes based on GGDB1.01 K2023-11-29Developing
GO-MFAnnotation for molecular functions as defined in the "Molecular Function" subtree of Gene Ontology19.7 K2023-12-04Testing
NCBITAXONannotation for NCBI taxonomy. Automatic annotation by PD-NCBITaxon.502 K2023-11-24Developing
performance-testa project for performance test480 K2023-11-27Testing
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
Automatic annotators
NameDescription
1-10 / 38 show all
PubTator-ChemicalTo pull the pre-computed chemical annotation from PubTator.
PubTator-GeneTo pull the pre-computed gene annotation from PubTator.
PubTator-SpeciesTo pull the pre-computed Species annotation from PubTator.
TextSentencersentence segmentation
PubTator-DiseaseTo pull the pre-computed disease annotation from PubTator.
PubTator-MutationTo pull the pre-computed mutation annotation from PubTator.
discourse-simplifierA discourse analyzer developed by Univ. Manchester.
PD-NGLY1-deficiency-BA batch annotator for NGLY1 deficiency
PD-UBERON-AEIt annotates for anatomical entities, based on the UBERON-AE dictionary on PubDictionaries. Threshold is set to 0.85.
PD-MONDOPubDictionaries annotation with the MONDO dictionary.
Editors
NameDescription
1-2 / 2
TextAE-oldTextAE version 4, which was the latest stable version until Apr. 19, 2020.
TextAETextAE version 5, which enables edition of attributes of denotations.