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User 'Jin-Dong Kim'


NameTDescription# Ann.Updated atStatus
31-40 / 47 show all
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
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
UBERON-AEAnnotation for anatomical entities based on the "Anatomical Entity" subtree of UBERON ontology. Annotations are automatically produced using PubDictionaries with threshold: 0.85.865 K2018-01-27Developing
genia-medco-corefCoreference annotation made to the Genia corpus, following the MUC annotation scheme. It is a product of the collaboration between the Genia and the MedCo projects.46.1 K2017-09-02Developing
GlycoBiology-Motifs4.15 K2017-09-09

Automatic annotators

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TextSentencersentence segmentation
EnjuParserEnju HPSG Parser developed by University of Tokyo.
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-UBERON-AEIt annotates for anatomical entities, based on the UBERON-AE dictionary on PubDictionaries. Threshold is set to 0.85.
PD-GlycoEpitope-BA batch annotator using PubDictionaries with the dictionary 'GlycoEpitope'
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.


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