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Jin-Dong Kim
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NameDescriptionUpdated at
11-12 / 12 show all
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
GlyCosmos15Collection of annotations to the abstracts from the following journals: Analytical_Chemistry Biochim_Biophys_Acta Carbohydrate_Research Cell Glycobiology Glycoconjugate_Journal J_Am_Chem_Soc Journal_of_Biological_Chemistry Journal_of_Proteome_Research Journal_of_Proteomics Molecular_and_Cellular_Proteomics Nature_Biotechnology Nature_Communications Nature_Methods Scientific_Reports 2024-09-19
Projects
NameTDescription# Ann.Updated atStatus
121-130 / 161 show all
GO-BPAnnotation for biological processes as defined in the "Biological Process" subset of Gene Ontology35.4 K2023-11-29Developing
GO-MFAnnotation for molecular functions as defined in the "Molecular Function" subtree of Gene Ontology19.7 K2023-12-04Testing
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
Glycosmos6-MATAutomatic annotation by PD-MAT.263 K2023-11-29Developing
GlycosmosP-GlycoEpitope242023-11-29Testing
sentencesSentence segmentation annotation. Automatic annotation by TextSentencer.6.96 M2023-11-24Developing
Test-Documents12023-11-24
GlyCosmosP-Glycan-Motif82023-11-24Developing
MENA-example232023-11-24Testing
Glycosmos6-GlycoEpitopeAutomatic annotation by PD-GlycoEpitope.19.9 K2023-11-28Developing
Automatic annotators
NameDescription
1-10 / 40 show all
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.
PubTator-DiseaseTo pull the pre-computed disease annotation from PubTator.
PubTator-MutationTo pull the pre-computed mutation annotation from PubTator.
discourse-simplifierA discourse analyzer developed by Univ. Manchester.
PD-NGLY1-deficiency-BA batch annotator for NGLY1 deficiency
PD-UBERON-AEIt annotates for anatomical entities, based on the UBERON-AE dictionary on PubDictionaries. Threshold is set to 0.85.
PD-MONDOPubDictionaries annotation with the MONDO dictionary.
PD-FMA-PAEPhysical Anatomical Entities from FMA
Editors
Name Description
1-1 / 1
TextAEThe official stable version of TextAE.