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User 'Jin-Dong Kim'

Collections

NameDescriptionUpdated at
1-4 / 4
GlycoBiologyAnnotations made to the titles and abstracts of the journal 'GlycoBiology'2019-03-10
PreeclampsiaPreeclampsia-related annotations for text mining2019-03-10
bionlp-st-ge-2016The 2016 edition of the Genia event extraction (GE) task organized within BioNLP-ST 20162019-03-11
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.2019-06-11

Projects

NameTDescription# Ann.Updated atStatus
1-10 / 62 show all
BioASQ-samplecollection of PubMed articles which appear in the BioASQ sample data set.02015-10-13Testing
DisGeNETDisease-Gene association annotation.3.12 M2016-01-28Beta
CHEMDNER-training-testThe training subset of the CHEMDNER corpus29.4 K2015-03-23Testing
pubtator-sampleSample annotation of PubTator produced by Zhiyong Lu et al.282016-01-19Testing
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 K2017-11-07Developing
GlycoBiology-FMAFMA ontology-based annotation to GlycoBiology abstracts96.3 K2016-01-31Testing
metamap-sampleSample annotation of MetaMep, produced by Aronson, et al. An overview of MetaMap: historical perspective and recent advances, JAMIA 201010.9 K2016-12-19Testing
uniprot-mouseProtein annotation based on UniProt11.5 K2016-04-27Developing
uniprot-humanUniprot proteins for human21.9 K2016-04-25Testing
GO-CCAnnotation for cellular components as defined in the "Cellular Component" subtree of Gene Ontology17.6 K2016-05-03Developing

Automatic annotators

NameDescription
1-10 / 23 show all
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-Preeclampsia-B
PD-GlycoEpitope-BA batch annotator using PubDictionaries with the dictionary 'GlycoEpitope'
PD-GlycoGenes-B
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.

Editors

NameDescription
1-2 / 2
TextAEIt is a "Text Annotation Editor" developed by DBCLS. It is developed as a model implementation of PubAnnotation-interoperable viewer/editor.
TextAE-DevIt is a development version of TextAE. While this version has richer features, there is a chance of some bugs.