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NameTDescription # Ann.AuthorMaintainerUpdated_atStatus

261-280 / 316 show all
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
PMA_MER PMAs annotated using MERpy.58.9 KStefano Rensitherightstef2023-11-29Developing
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
AlvisNLP-Test Project for testing AlviNLP PubAnnotation server during BLAH3.17Bibliome2023-11-29Testing
Trait curation Project for trait curation in PGDBj479Sachiko ShirasawaSachiko Shirasawa2023-11-24Testing
ykjeong_test pub_annotation_test2762023-11-28Testing
LitCovid_Glycan-Motif-Structure PubDictionaries annotation for glycan-Motif terms.6.51 KISSAKU YAMADA2023-11-29Beta
QFMC_MEDLINE Quaero French Medical Corpus: Annotation of MEDLINE titles5.9 KAurélie NévéolPierre Zweigenbaum2023-11-29Beta
metamap-sample Sample annotation of MetaMep, produced by Aronson, et al. An overview of MetaMap: historical perspective and recent advances, JAMIA 201010.9 KAlan R AronsonJin-Dong Kim2023-11-27Testing
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 KRindflesch et al.Jin-Dong Kim2023-11-29Testing
PubMed_Structured_Abstracts Sections (zones) as retrieved from PubMed.131 Kzebet2023-11-28Released
disease_gene_microbe_small Small version (48 abstract that mention both Crohns and S. aureus) for development purposes Abbreviation: dgm Content: annotated abstracts on Crohn’s disease or on on Staphylococcus aureus (according to the jensenlab.org indexing resources) Entity types: (three for a start, organisms (NCBI Taxonomy taxa), disease (Disease Ontology terms), human genes (ENSEMBL proteins) Aim: Explore indirect associations of diseases to microbial species in this corpus via gene co-mentions536evangelos2023-11-27Testing
SPECIES800 SPECIES 800 (S800): an abstract-based manually annotated corpus. S800 comprises 800 PubMed abstracts in which organism mentions were identified and mapped to the corresponding NCBI Taxonomy identifiers. Described in: The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. Pafilis E, Frankild SP, Fanini L, Faulwetter S, Pavloudi C, et al. (2013). PLoS ONE, 2013, 8(6): e65390. doi:10.1371/journal.pone.00653903.71 KEvangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensenevangelos2023-11-28Released
Test190926 test0Takeru Nakazatonakazato2023-11-29Testing
ichiharatest_150825_2 test0ichihara_hisakoHisako Ichihara2015-09-11Testing
ichiharatest_150830_1 test99Hisako Ichihara2023-11-29Testing
ichiharatest_150825 test0ichihara_hisakoHisako Ichihara2023-11-29Testing
ichiharatest_150825_3 test0ichihara_hisakoHisako Ichihara2023-11-26Testing
falsetest_150825 test0ichihara_hisakoHisako Ichihara2015-09-11Testing
test1 test121H. S. ParkSophie Nam2023-11-26Testing
NameT# Ann.AuthorMaintainerUpdated_atStatus

261-280 / 316 show all
bionlp-st-ge-2016-test 7.99 KDBCLSJin-Dong Kim2023-11-29Released
PMA_MER 58.9 KStefano Rensitherightstef2023-11-29Developing
bionlp-st-ge-2016-test-proteins 4.34 KDBCLSJin-Dong Kim2023-11-27Released
AlvisNLP-Test 17Bibliome2023-11-29Testing
Trait curation 479Sachiko ShirasawaSachiko Shirasawa2023-11-24Testing
ykjeong_test 2762023-11-28Testing
LitCovid_Glycan-Motif-Structure 6.51 KISSAKU YAMADA2023-11-29Beta
QFMC_MEDLINE 5.9 KAurélie NévéolPierre Zweigenbaum2023-11-29Beta
metamap-sample 10.9 KAlan R AronsonJin-Dong Kim2023-11-27Testing
semrep-sample 11.1 KRindflesch et al.Jin-Dong Kim2023-11-29Testing
PubMed_Structured_Abstracts 131 Kzebet2023-11-28Released
disease_gene_microbe_small 536evangelos2023-11-27Testing
SPECIES800 3.71 KEvangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensenevangelos2023-11-28Released
Test190926 0Takeru Nakazatonakazato2023-11-29Testing
ichiharatest_150825_2 0ichihara_hisakoHisako Ichihara2015-09-11Testing
ichiharatest_150830_1 99Hisako Ichihara2023-11-29Testing
ichiharatest_150825 0ichihara_hisakoHisako Ichihara2023-11-29Testing
ichiharatest_150825_3 0ichihara_hisakoHisako Ichihara2023-11-26Testing
falsetest_150825 0ichihara_hisakoHisako Ichihara2015-09-11Testing
test1 21H. S. ParkSophie Nam2023-11-26Testing