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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
31-40 / 58 show all
examplean example project to demonstrate the functionality of PubAnnotation5522019-02-11Testing
pubmed-sentences-benchmarkA benchmark data for text segmentation into sentences. The source of annotation is the GENIA treebank v1.0. Following is the process taken. began with the GENIA treebank v1.0. sentence annotations were extracted and converted to PubAnnotation JSON. uploaded. 12 abstracts met alignment failure. among the 12 failure cases, 4 had a dot('.') character where there should be colon (':'). They were manually fixed then successfully uploaded: 7903907, 8053950, 8508358, 9415639. among the 12 failed abstracts, 8 were "250 word truncation" cases. They were manually fixed and successfully uploaded. During the fixing, manual annotations were added for the missing pieces of text. 30 abstracts had extra text in the end, indicating copyright statement, e.g., "Copyright 1998 Academic Press." They were annotated as a sentence in GTB. However, the text did not exist anymore in PubMed. Therefore, the extra texts were removed, together with the sentence annotation to them. 18.5 K2017-08-15Released
PubMed-2017abstracts published in 2017.02017-09-01Developing
DisGeNet-2017-sample2.93 K2017-09-25Testing
Preeclampsia-compare67.4 K2019-01-31Testing
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 K2019-07-15Testing
GlycoGenesannotation for glyco-genes based on GGDB1.01 K2017-09-15Developing
PubMed-2000abstracts published in 2000.02017-09-01Developing
PubMed-2010abstracts published in 201002017-09-01
performance-testa project for performance test487 K2018-07-15Testing

Automatic annotators

NameDescription
1-10 / 21 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.