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User 'Jin-Dong Kim'

Collections

Name		Description	Updated at

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GlycoBiology		Annotations made to the titles and abstracts of the journal 'GlycoBiology'	2019-03-10
Preeclampsia		Preeclampsia-related annotations for text mining	2019-03-10
bionlp-st-ge-2016		The 2016 edition of the Genia event extraction (GE) task organized within BioNLP-ST 2016	2019-03-11
GlyCosmos600		A 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.	2021-10-22
LitCovid-v1		This collection includes the result from the Covid-19 Virtual Hackathon. LitCovid is a comprehensive literature resource on the subject of Covid-19 collected by NCBI: https://www.ncbi.nlm.nih.gov/research/coronavirus/ Since the literature dataset was released, several groups are producing annotations to the dataset. To facilitate a venue for aggregating the valuable resources which are highly relevant to each other, and should be much more useful when they can be accessed together, this PubAnnotation collection is set up. It is a part of the Covid19-PubAnnotation project. In this collection, the LitCovid-docs project contains all the documents contained in the LitCovid literature collection, and the other projects are annotation datasets contributed by various groups. It is an open collection, which means anyone who wants to contribute can do so, in the following way: take the documents in the, LitCovid-docs project produce annotation to the texts based on your resource, and contribute the annotation back to this collection: create your own project at PubAnnotaiton, upload your annotation to the project (HowTo), and add the project to this collection. All the contributed annotations will become publicly available. Please note that, during uploading your annotation data, you do not need to be worried about slight changes in the text: PubAnnotation will automatically catch them and adjust the positions appropriately. Should you have any question, please feel free to mail to admin@pubannotation.org.	2020-11-20
LitCovid-sample		Various annotations to a sample set of LitCovid, to demonstrate potential of harmonized various annotations.	2021-01-14
CORD-19-sample-annotation			2020-04-21
LitCovid			2021-10-18
LitCoin			2021-12-14
LitCoin-Test			2021-12-23

Projects

Name	T	Description	# Ann.	Updated at	Status

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CORD-19_bioRxiv_medRxiv_subset		The bioRxiv/medRxiv subset of the CORD-19 dataset: pre-prints that are not peer reviewed. The documents in this project will be updated as the CORD-19 dataset grows. See the COVID DATASET LICENSE AGREEMENT.	0	2020-03-23	Released
CORD-19_Commercial_use_subset		The Commercial use subset of the CORD-19 dataset. The documents in this project will be updated as the CORD-19 dataset grows. See the COVID DATASET LICENSE AGREEMENT.	0	2020-03-23	Released
CORD-19_Custom_license_subset		The Custom license subset of the CORD-19 dataset. The documents in this project will be updated as the CORD-19 dataset grows. See the COVID DATASET LICENSE AGREEMENT.	5.08 M	2020-04-10	Released
CORD-19_Non-commercial_use_subset		The Non commercial use subset of the CORD-19 dataset. The documents in this project will be updated as the CORD-19 dataset grows. See the COVID DATASET LICENSE AGREEMENT.	0	2020-03-23	Released
bionlp-st-ge-2016-uniprot		UniProt protein annotation to the benchmark data set of BioNLP-ST 2016 GE task: reference data set (bionlp-st-ge-2016-reference) and test data set (bionlp-st-ge-2016-test). The annotations are produced based on a dictionary which is semi-automatically compiled for the 34 full paper articles included in the benchmark data set (20 in the reference data set + 14 in the test data set). For detailed information about BioNLP-ST GE 2016 task data sets, please refer to the benchmark reference data set (bionlp-st-ge-2016-reference) and benchmark test data set (bionlp-st-ge-2016-test).	16.2 K	2020-10-02	Beta
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
pubtator-sample		Sample annotation of PubTator produced by Zhiyong Lu et al.	28	2020-11-16	Testing
semrep-sample		Sample annotation of SemRep, produced by Rindflesch, et al. Rindflesch, T.C. and Fiszman, M. (2003). The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. Journal of Biomedical Informatics, 36(6):462-477.	11.1 K	2017-07-15	Testing
sentences		Sentence segmentation annotation	6.96 M	2022-10-20	Developing
LitCovid-sentences-v1		Sentence segmentation of all the texts in the LitCovid literature. The segmentation is automatically obtained using the TextSentencer annotation service developed and maintained by DBCLS.	16.5 K	2021-01-17	Released

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.