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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
141-150 / 160 show all
test102122023-11-24
PubMed-German-testA collection of PubMed abstracts which are written in German02023-11-24Developing
PubMed-2017abstracts published in 2017.02023-11-24Developing
speech-test62023-11-26Testing
CORD-19-SciBite-sentences11.2 K2023-11-26Testing
LitCovid-PD-FMA-UBERON-v1PubDictionaries annotation for anatomy terms - updated at 2020-04-20 Disease term annotation based on FMA and Uberon. Version 2020-04-20. The terms in FMA and Uberon are loaded in PubDictionaries (FMA and Uberon), with which the annotations in this project are produced. The parameter configuration used for this project is here for FMA and there for Uberon. 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.4.3 K2023-11-27Released
bionlp-st-ge-2016-test-proteinsProtein annotations to the benchmark test data set of the BioNLP-ST 2016 GE task. A participant of the GE task may import the documents and annotations of this project to his/her own project, to begin with producing event annotations. For more details, please refer to the benchmark test data set (bionlp-st-ge-2016-test). 4.34 K2023-11-27Released
GlyCosmos600-GlycoProteinsGlycoProtein annotations were made using the glycoprotein-name dictionary on PubDictionaries: http://pubannotation.org/projects/GlyCosmos600-docs The documents were imported from the GlyCosmos600-docs project: http://pubannotation.org/projects/GlyCosmos600-docs3.68 K2023-11-27Testing
GlyCosmos6-Glycan-Image1.95 K2024-05-17Developing
bionlp-st-ge-2016-corefCoreference annotation to the benchmark data set (reference and test) of BioNLP-ST 2016 GE task. For detailed information, please refer to the benchmark reference data set (bionlp-st-ge-2016-reference) and benchmark test data set (bionlp-st-ge-2016-test).8532023-11-28Released
Automatic annotators
NameDescription
1-10 / 39 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
Name Description
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.