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Name TDescription# Ann.AuthorMaintainerUpdated_atStatus

61-80 / 556 show all
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
bionlp-st-ge-2016-reference-eval 426Jin-Dong Kim2023-11-29Testing
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
bionlp-st-ge-2016-spacy-parsed Dependency parses produced by spaCy parser, and part-of-speech tags produced by Stanford tagger (with the wsj-0-18-left3words-nodistsim model). The exact procedure is described here. Data set contains the 34 full paper articles used in the BioNLP 2016 GE task. 225 KNico ColicNico Colic2023-11-29Released
bionlp-st-ge-2016-test It is the benchmark test data set of the BioNLP-ST 2016 GE task. It includes Genia-style event annotations to 14 full paper articles which are about NFκB proteins. For testing purpose, however, annotations are all blinded, which means users cannot see the annotations in this project. Instead, annotations in any other project can be compared to the hidden annotations in this project, then the annotations in the project will be automatically evaluated based on the comparison. A participant of GE task can get the evaluation of his/her result of automatic annotation, through following process: Create a new project. Import documents from the project, bionlp-st-2016-test-proteins to your project. Import annotations from the project, bionlp-st-2016-test-proteins to your project. At this point, you may want to compare you project to this project, the benchmark data set. It will show that protein annotations in your project is 100% correct, but other annotations, e.g., events, are 0%. Produce event annotations, using your system, upon the protein annotations. Upload your event annotations to your project. Compare your project to this project, to get evaluation. GE 2016 benchmark data set is provided as multi-layer annotations which include: bionlp-st-ge-2016-reference: benchmark reference data set bionlp-st-ge-2016-test: benchmark test data set (this project) 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.7.99 KDBCLSJin-Dong Kim2023-11-29Released
bionlp-st-ge-2016-test-ihmc 14.4 KLucian Galescu2023-11-29Testing
bionlp-st-ge-2016-test-proteins Protein annotations to the benchmark test data set of the BioNLP-ST 2016 GE task. A participant of the GE task may import the documents and annotations of this project to his/her own project, to begin with producing event annotations. For more details, please refer to the benchmark test data set (bionlp-st-ge-2016-test). 4.34 KDBCLSJin-Dong Kim2023-11-27Released
bionlp-st-ge-2016-test-tees NER and event extraction produced by TEES (with the default GE11 model) for the 14 full papers used in the BioNLP 2016 GE task test corpus.9.17 KNico ColicNico Colic2023-11-29Released
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
bionlp-st-gro-2013-development The development data set of the BioNLP-ST 2013 GRO task, including 50 MEDLINE abstracts that are annotated with concepts and relations of the Gene Regulation Ontology (GRO; http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html)2.66 KJung-jae KimJung-jae Kim2023-11-29Testing
bionlp-st-gro-2013-training The training data set of the BioNLP-ST 2013 GRO task, including 150 MEDLINE abstracts that are annotated with concepts and relations of the Gene Regulation Ontology (GRO; http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html)8.02 KJung-jae KimJung-jae Kim2023-11-29Testing
bionlp-st-id-2011-training The training dataset from the infectious diseases (ID) task in the BioNLP Shared Task 2011. Entity types: - Genes and gene products: gene, RNA, and protein name mentions. - Two-component systems: mentions of the names of two-component regulatory systems, frequently embedding the names of the two Proteins forming the system.- Chemicals: mentions of chemical compounds such as "NaCL".- Organisms: mentions of organism names or organism specification through specific properties (e.g. "graRS mutant").- Regulons/Operons: mentions of names of specific regulons and operons.5.61 KUniversity of Tokyo Tsujii Laboratory, NaCTeM and Biocomplexity Institute of Virginia TechYue Wang2023-11-28Released
bionlp-st-pc-2013-training The training dataset from the pathway curation (PC) task in the BioNLP Shared Task 2013. The entity types defined in the PC task are simple chemical, gene or gene product, complex and cellular component.7.86 KNaCTeM and KISTIYue Wang2023-11-27Released
biosemtest test submitting Peregrine annotations35.6 KMark Thompsonmarkthompson2023-11-29Testing
Biotea NCBO annotation on full text for PMC articles. Currently including only a small set of 2811 articles corresponding to those supporting curated diesease-protein annotation from UniProt and with machine-processable full text.894 KL. Garcia2023-11-24Developing
BLAH2015_Annotations_Adderall 0nestoralvaronestoralvaro2023-11-29Testing
BLAH2015_Annotations_test_5 1.34 Knestoralvaronestoralvaro2023-11-30Testing
BLAH2021-glytoucan-iupac 0kiyoko2021-01-19
blah6 device Annotator374slee72682023-11-28Testing
blah6_medical_device BLAH6 hackathon project to annotate medical device indications in premarket approval statement summaries. The documents in this project serve as a corpus of premarket approval (PMA) statements that have undergone quality control. In particular, we have (1) removed non-ascii characters, (2) fixed some text segmentation errors, and (3) fixed some capitalization errors.0Stefano Rensitherightstef2023-11-29Beta
Name T# Ann.AuthorMaintainerUpdated_atStatus

61-80 / 556 show all
bionlp-st-ge-2016-reference 14.4 KDBCLSJin-Dong Kim2023-11-29Released
bionlp-st-ge-2016-reference-eval 426Jin-Dong Kim2023-11-29Testing
bionlp-st-ge-2016-reference-tees 14.6 KNico Colic Nico Colic2023-11-29Released
bionlp-st-ge-2016-spacy-parsed 225 KNico ColicNico Colic2023-11-29Released
bionlp-st-ge-2016-test 7.99 KDBCLSJin-Dong Kim2023-11-29Released
bionlp-st-ge-2016-test-ihmc 14.4 KLucian Galescu2023-11-29Testing
bionlp-st-ge-2016-test-proteins 4.34 KDBCLSJin-Dong Kim2023-11-27Released
bionlp-st-ge-2016-test-tees 9.17 KNico ColicNico Colic2023-11-29Released
bionlp-st-ge-2016-uniprot 16.2 KDBCLSJin-Dong Kim2023-11-29Beta
bionlp-st-gro-2013-development 2.66 KJung-jae KimJung-jae Kim2023-11-29Testing
bionlp-st-gro-2013-training 8.02 KJung-jae KimJung-jae Kim2023-11-29Testing
bionlp-st-id-2011-training 5.61 KUniversity of Tokyo Tsujii Laboratory, NaCTeM and Biocomplexity Institute of Virginia TechYue Wang2023-11-28Released
bionlp-st-pc-2013-training 7.86 KNaCTeM and KISTIYue Wang2023-11-27Released
biosemtest 35.6 KMark Thompsonmarkthompson2023-11-29Testing
Biotea 894 KL. Garcia2023-11-24Developing
BLAH2015_Annotations_Adderall 0nestoralvaronestoralvaro2023-11-29Testing
BLAH2015_Annotations_test_5 1.34 Knestoralvaronestoralvaro2023-11-30Testing
BLAH2021-glytoucan-iupac 0kiyoko2021-01-19
blah6 374slee72682023-11-28Testing
blah6_medical_device 0Stefano Rensitherightstef2023-11-29Beta