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NameTDescription# Ann. AuthorMaintainerUpdated_atStatus

481-500 / 592 show all
LitCoin-entities 13.6 KJin-Dong Kim2023-11-29Testing
GlyCosmos600-FMA 13.8 KJin-Dong Kim2024-09-28
LitCoin-PubTator-for-Tuning A set of randomly selected PubMed articles with PubTator annotation. The labels of PubTator annotations are converted to corresponding labels for LitCoin as follows: 'Gene' -> 'GeneOrGeneProduct', 'Disease' -> 'DiseaseOrPhenotypicFeature', 'Chemical' -> 'ChemicalEntity' 'Species' -> 'OrganismTaxon' 'Mutation' -> 'SequenceVariant' 'CellLine' -> 'CellLine'14.2 KJin-Dong Kim2023-11-29
bionlp-st-ge-2016-test-ihmc 14.4 KLucian Galescu2023-11-29Testing
bionlp-st-ge-2016-reference It 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 KDBCLSJin-Dong Kim2023-11-29Released
events-check-again 14.4 K2023-11-30Testing
bionlp-st-ge-2016-reference-tees NER and event extraction produced by TEES (with the default GE11 model) for the 20 full papers used in the BioNLP 2016 GE task reference corpus.14.6 KNico Colic Nico Colic2023-11-29Released
LitCoin-training-merged 14.8 KJin-Dong Kim2023-11-24
LitCoin-GeneOrGeneProduct-v0 https://pubdictionaries.org/text_annotation.json?dictionary=NCBIGene-NER&threshold=0.85&abbreviation=true15.8 KJin-Dong Kim2023-11-29
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 KDBCLSJin-Dong Kim2023-11-29Beta
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 KJin-Dong Kim2023-11-27Released
testtesttest 17.4 KJin-Dong Kim2024-09-16Developing
GO-CC Annotation for cellular components as defined in the "Cellular Component" subtree of Gene Ontology17.6 KDBCLSJin-Dong Kim2023-11-30Developing
test-210614 17.8 KJin-Dong Kim2024-01-05Testing
preeclampsia_genes 17.8 KJin-Dong Kim2023-11-29Developing
pubmed-sentences-benchmark A 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. 18.4 KGENIA projectJin-Dong Kim2023-11-28Released
sonoma _19.3 KStandigm2023-11-24Testing
GO-MF Annotation for molecular functions as defined in the "Molecular Function" subtree of Gene Ontology19.7 KDBCLSJin-Dong Kim2023-12-04Testing
Nanbyo-330-20171127 Disease descriptions extracted from MHLW19.8 KToyofumi Fujiwara2023-11-26Testing
Glycosmos6-GlycoEpitope Automatic annotation by PD-GlycoEpitope.19.9 KJin-Dong Kim2023-11-28Developing
NameT# Ann. AuthorMaintainerUpdated_atStatus

481-500 / 592 show all
LitCoin-entities 13.6 KJin-Dong Kim2023-11-29Testing
GlyCosmos600-FMA 13.8 KJin-Dong Kim2024-09-28
LitCoin-PubTator-for-Tuning 14.2 KJin-Dong Kim2023-11-29
bionlp-st-ge-2016-test-ihmc 14.4 KLucian Galescu2023-11-29Testing
bionlp-st-ge-2016-reference 14.4 KDBCLSJin-Dong Kim2023-11-29Released
events-check-again 14.4 K2023-11-30Testing
bionlp-st-ge-2016-reference-tees 14.6 KNico Colic Nico Colic2023-11-29Released
LitCoin-training-merged 14.8 KJin-Dong Kim2023-11-24
LitCoin-GeneOrGeneProduct-v0 15.8 KJin-Dong Kim2023-11-29
bionlp-st-ge-2016-uniprot 16.2 KDBCLSJin-Dong Kim2023-11-29Beta
LitCovid-sentences-v1 16.5 KJin-Dong Kim2023-11-27Released
testtesttest 17.4 KJin-Dong Kim2024-09-16Developing
GO-CC 17.6 KDBCLSJin-Dong Kim2023-11-30Developing
test-210614 17.8 KJin-Dong Kim2024-01-05Testing
preeclampsia_genes 17.8 KJin-Dong Kim2023-11-29Developing
pubmed-sentences-benchmark 18.4 KGENIA projectJin-Dong Kim2023-11-28Released
sonoma 19.3 KStandigm2023-11-24Testing
GO-MF 19.7 KDBCLSJin-Dong Kim2023-12-04Testing
Nanbyo-330-20171127 19.8 KToyofumi Fujiwara2023-11-26Testing
Glycosmos6-GlycoEpitope 19.9 KJin-Dong Kim2023-11-28Developing