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Jin-Dong Kim
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NameDescriptionUpdated at
11-12 / 12 show all
CORD-19CORD-19 (COVID-19 Open Research Dataset) is a free, open resource for the global research community provided by the Allen Institute for AI: https://pages.semanticscholar.org/coronavirus-research. As of 2020-03-20, it contains over 29,000 full text articles. This CORD-19 collection at PubAnnotation is prepared for the purpose of collecting annotations to the texts, so that they can be easily accessed and utilized. If you want to contribute with your annotation, take the documents in the CORD-19_All_docs project, produce your annotation to the texts using your annotation system, and contribute the annotation back to PubAnnotation (HowTo). 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. Once you have uploaded your annotation, please notify it to admin@pubannotation.org admin@pubannotation.org, so that it can be included in this collection, which will make your annotation much easily findable. Note that as the CORD-19 dataset grows, the documents in this collection also will be updated. IMPORTANT: CORD-19 License agreement requires that the dataset must be used for text and data mining only.2020-04-14
Glycosmos6This 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 2023-11-16
Projects
NameTDescription# Ann.Updated at Status
71-80 / 160 show all
LitCovid-sample-HP02023-11-29Testing
GlycoBiology-Motifs4.15 K2023-11-29
CORD-19-PD-HPPubDictionaries annotation for HP terms - updated at 2020-04-30 Disease term annotation based on HP. Version 2020-04-20. The terms in HP are loaded in PubDictionaries, with which the annotations in this project are produced. The parameter configuration used for this project is here. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.1.15 M2023-11-29Released
ggdb-test2.4 K2023-11-29Testing
EDAM-topicsannotation for EDAM topics11.6 K2023-11-29Testing
bionlp-st-ge-2016-referenceIt is the benchmark reference data set of the BioNLP-ST 2016 GE task. It includes Genia-style event annotations to 20 full paper articles which are about NFκB proteins. The task is to develop an automatic annotation system which can produce annotation similar to the annotation in this data set as much as possible. For evaluation of the performance of a participating system, the system needs to produce annotations to the documents in the benchmark test data set (bionlp-st-ge-2016-test). GE 2016 benchmark data set is provided as multi-layer annotations which include: bionlp-st-ge-2016-reference: benchmark reference data set (this project) bionlp-st-ge-2016-test: benchmark test data set (annotations are blined) bionlp-st-ge-2016-test-proteins: protein annotation to the benchmark test data set Following is supporting resources: bionlp-st-ge-2016-coref: coreference annotation bionlp-st-ge-2016-uniprot: Protein annotation with UniProt IDs. pmc-enju-pas: dependency parsing result produced by Enju UBERON-AE: annotation for anatomical entities as defined in UBERON ICD10: annotation for disease names as defined in ICD10 GO-BP: annotation for biological process names as defined in GO GO-CC: annotation for cellular component names as defined in GO A SPARQL-driven search interface is provided at http://bionlp.dbcls.jp/sparql.14.4 K2023-11-29Released
bionlp-st-ge-2016-reference-eval4262023-11-29Testing
Test-merged3.21 K2023-11-29
LitCoin-entities13.6 K2023-11-29Testing
LitCovid-PD-HP-v1PubDictionaries annotation for human phenotype terms - updated at 2020-04-20 Disease term annotation based on HP. Version 2020-04-20. The terms in HP are loaded in PubDictionaries, with which the annotations in this project are produced. The parameter configuration used for this project is here. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.3.03 K2023-11-29Released
Automatic annotators
NameDescription
21-30 / 39 show all
PD-NCBITaxon-B
PubTatorPubTator annotation provided by NCBI
PD-CHEBI-B
PD-GlycoGenes20190927-B
PD-GO-BP-BBiological Processes as defined in GO
PD-HP-B
PD-HP
PD-CLO-B
PD-HP-PA-B
PD-HP-PA
Editors
NameDescription
1-2 / 2
TextAE-oldTextAE version 4, which was the latest stable version until Apr. 19, 2020.
TextAETextAE version 5, which enables edition of attributes of denotations.