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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
21-30 / 159 show all
NCBITAXONannotation for NCBI taxonomy. Automatic annotation by PD-NCBITaxon.502 K2023-11-24Developing
performance-testa project for performance test480 K2023-11-27Testing
LitCovid-TimeML426 K2023-11-29Developing
LitCovid-PD-GO-BPTerms for biological prosesses, as defined in GO374 K2023-11-29Developing
Glycosmos6-MATAutomatic annotation by PD-MAT.263 K2023-11-29Developing
mondo_diseaseannotation for diseases and disorders as defined in MONDO. Automatic annotation by PD-MONDO.256 K2023-11-28Developing
pmc-enju-pasPredicate-argument structure annotation produced by Enju. This data set is initially produced as a supporting resource for BioNLP-ST 2016 GE task. As so, it currently includes the 34 full paper articles that are in the benchmark data sets of GE 2016 task, reference data set (bionlp-st-ge-2016-reference) and test data set (bionlp-st-ge-2016-test), but will be extended to include more papers from the PubMed Central Open Access subset (PMCOA). 205 K2023-11-28Developing
LitCovid-PAS-EnjuPredicate-argument structure annotation produced by the Enju parser.125 K2023-11-28Beta
GlyCosmos6-Glycan-Motif-StructureAutomatic annotation by Covid-19_Glycan-Motif.107 K2023-11-24Developing
GlycoBiology-FMAFMA ontology-based annotation to GlycoBiology abstracts96.3 K2023-11-29Testing
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.