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User 'Jin-Dong Kim'

Collections

Name		Description	Updated at

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Glycosmos6		This 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	2022-02-21
LitCovid-sample		Various annotations to a sample set of LitCovid, to demonstrate potential of harmonized various annotations.	2021-01-14

Projects

Name	T	Description	# Ann.	Updated at	Status

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Test-Documents			0	2021-12-23
BioASQ-sample		collection of PubMed articles which appear in the BioASQ sample data set.	0	2015-10-13	Testing
LitCovid-sample-PD-MAT			251	2021-01-14	Developing
CHEMDNER-training-test		The training subset of the CHEMDNER corpus	29.4 K	2015-03-23	Testing
NCBITAXON		annotation for NCBI taxonomy	491 K	2022-10-20	Developing
pubtator-sample		Sample annotation of PubTator produced by Zhiyong Lu et al.	28	2020-11-16	Testing
speech-test			6	2022-04-17	Testing
GlycoBiology-FMA		FMA ontology-based annotation to GlycoBiology abstracts	96.3 K	2020-02-05	Testing
LitCovid-sample-Glycan			3.21 K	2021-01-19	Testing
metamap-sample		Sample annotation of MetaMep, produced by Aronson, et al. An overview of MetaMap: historical perspective and recent advances, JAMIA 2010	10.9 K	2016-12-19	Testing

Automatic annotators

Name	Description

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PubTator-Chemical	To pull the pre-computed chemical annotation from PubTator.
PubTator-Gene	To pull the pre-computed gene annotation from PubTator.
PubTator-Species	To pull the pre-computed Species annotation from PubTator.
TextSentencer	sentence segmentation
PubTator-Disease	To pull the pre-computed disease annotation from PubTator.
PubTator-Mutation	To pull the pre-computed mutation annotation from PubTator.
discourse-simplifier	A discourse analyzer developed by Univ. Manchester.
PD-NGLY1-deficiency-B	A batch annotator for NGLY1 deficiency
PD-UBERON-AE	It annotates for anatomical entities, based on the UBERON-AE dictionary on PubDictionaries. Threshold is set to 0.85.
PD-MONDO	PubDictionaries annotation with the MONDO dictionary.

Editors

Name	Description

1-3 / 3
TextAE-old	TextAE version 4, which was the latest stable version until Apr. 19, 2020.
TextAE-Dev	It is a development version of TextAE. While this version has richer features, there is a chance of some bugs.
TextAE	TextAE version 5, which enables edition of attributes of denotations.