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NameTDescription# Ann.AuthorMaintainer Updated_atStatus

1-20 / 227 show all
Find2ERFind the Findings of Enzymatic Reaction0Akihiro KamedaAkihiro Kameda2015-02-20Testing
Lectin3.52 Kangata2018-02-09
AlvisNLP-TestProject for testing AlviNLP PubAnnotation server during BLAH3.17Bibliome2017-01-20Testing
SNPPhenoExt3behrouz bokharaeianbokharaeian2016-04-30Developing
PreeclampsiaA collection of titles and abstracts of "Preeclampsia"-related papers. They were extracted from PubMed using the MeSH term "Preeclampsia" and specifying the language to be "English, on 11th September, 2017. The texts were then annotated by PubDictionaries using the dictionary "Preeclampsia".58.9 Kcallahan_tiff2019-01-30Developing
tmVarCorpusWei C-H, Harris BR, Kao H-Y, Lu Z (2013) tmVar: A text mining approach for extracting sequence variants in biomedical literature, Bioinformatics, 29(11) 1433-1439, doi:10.1093/bioinformatics/btt156.1.43 KChih-Hsuan Wei , Bethany R. Harris , Hung-Yu Kao and Zhiyong LuChih-Hsuan Wei2015-08-06Released
Test_PubTator62Chih-Hsuan Wei2016-04-20Testing
NCBIDiseaseCorpusThe NCBI disease corpus is fully annotated at the mention and concept level to serve as a research resource for the biomedical natural language processing community.6.88 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2015-08-06Released
Ab3P-abbreviationsThis corpus was developed during the creation of the Ab3P abbreviation definition identification tool. It includes 1250 manually annotated MEDLINE records. This gold standard includes 1221 abbreviation-definition pairs. Abbreviation definition identification based on automatic precision estimates Sunghwan Sohn, Donald C Comeau, Won Kim and W John Wilbur BMC Bioinformatics20089:402 DOI: 10.1186/1471-2105-9-4022.34 KSunghwan Sohn, Donald C Comeau, Won Kim and W John Wilburcomeau2016-07-29Beta
craft-sa-devDevelopment data for CRAFT SA shared task. This project contains the development (training) annotations for the Structural Annotation task of the CRAFT Shared Task 2019. This particular set contains token and sentence annotations with tokens linked via dependency relations. These dependency relations were automatically generated using the manually curated CRAFT constituency treebank files as input.512 KUniversity of Colorado Anschutz Medical Campuscraft-st2019-03-25Released
craft-ca-core-devDevelopment data for CRAFT CA shared task, core concepts only. This project contains the development (training) annotations for the Concept Annotation task of the CRAFT Shared Task 2019. This particular set of concept annotations is the "core" set. See the task description for details, but this set contains only annotations to concepts that appear in the original 10 Open Biomedical Ontologies used for annotation. (That is to say, it does not contain any annotations to extension classes).62.3 KUniversity of Colorado Anschutz Medical Campuscraft-st2019-03-25Released
craft-ca-core-ex-devDevelopment data for CRAFT CA shared task, core concepts + EXTENSIONS. This project contains the development (training) annotations for the Concept Annotation task of the CRAFT Shared Task 2019. This particular set of concept annotations is the "core+extensions" set. See the task description for details, but this set contains annotations to concepts that appear in the original 10 Open Biomedical Ontologies used for annotation PLUS annotations to extension classes created using the core concepts.94.3 KUniversity of Colorado Anschutz Medical Campuscraft-st2019-03-25Released
DLUT931DLUT NLP Lab.Test our event extration result for 16 GE task.4.57 KDLUT9312016-05-17Testing
test010Erika Asamizu2015-09-11Testing
Erin_test@ Yonsei University0ErinErinHJ_Kim2017-07-13Testing
bionlp-st-2016-SeeDev-devEntities and event annotations from the development set of the BioNLP-ST 2016 SeeDev task. SeeDev task focuses on seed storage and reserve accumulation on the model organism, Arabidopsis thaliana. The SeeDev task is based on the knowledge model Gene Regulation Network for Arabidopsis (GRNA) that meets the needs of text-mining (i.e. manual annotation of texts and automatic information extraction), experimental data indexing and retrieval and reuse in other plant systems. It is also expected to meet the requirements of the integration of the text knowledge with knowledge derived from experimental data in view of modeling in systems biology. GRNA model defines 16 different types of entities, and 22 types of event (in five sets of event types) that may be combined in complex events. For more information, please refer to the task website All annotations : Train set Development set Test set (without events) 61EstelleChaix2018-01-13Released
bionlp-st-2016-SeeDev-testEntities annotations from the test set of the BioNLP-ST 2016 SeeDev task. SeeDev task focuses on seed storage and reserve accumulation on the model organism, Arabidopsis thaliana. The SeeDev task is based on the knowledge model Gene Regulation Network for Arabidopsis (GRNA) that meets the needs of text-mining (i.e. manual annotation of texts and automatic information extraction), experimental data indexing and retrieval and reuse in other plant systems. It is also expected to meet the requirements of the integration of the text knowledge with knowledge derived from experimental data in view of modeling in systems biology. GRNA model defines 16 different types of entities, and 22 types of event (in five sets of event types) that may be combined in complex events. For more information, please refer to the task website All annotations : Train set Development set Test set (without events) 184EstelleChaix2018-01-13Released
bionlp-st-2016-SeeDev-trainingEntities and event annotations from the training set of the BioNLP-ST 2016 SeeDev task. SeeDev task focuses on seed storage and reserve accumulation on the model organism, Arabidopsis thaliana. The SeeDev task is based on the knowledge model Gene Regulation Network for Arabidopsis (GRNA) that meets the needs of text-mining (i.e. manual annotation of texts and automatic information extraction), experimental data indexing and retrieval and reuse in other plant systems. It is also expected to meet the requirements of the integration of the text knowledge with knowledge derived from experimental data in view of modeling in systems biology. GRNA model defines 16 different types of entities, and 22 types of event (in five sets of event types) that may be combined in complex events. For more information, please refer to the task website All annotations : Train set Development set Test set (without events) 35EstelleChaix2018-01-13Released
SPECIES800SPECIES 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 Jensenevangelos2018-04-25Released
disease_gene_microbe_smallSmall 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-mentions536evangelos2018-01-13Testing
NameT# Ann.AuthorMaintainer Updated_atStatus

1-20 / 227 show all
Find2ER0Akihiro KamedaAkihiro Kameda2015-02-20Testing
Lectin3.52 Kangata2018-02-09
AlvisNLP-Test17Bibliome2017-01-20Testing
SNPPhenoExt3behrouz bokharaeianbokharaeian2016-04-30Developing
Preeclampsia58.9 Kcallahan_tiff2019-01-30Developing
tmVarCorpus1.43 KChih-Hsuan Wei , Bethany R. Harris , Hung-Yu Kao and Zhiyong LuChih-Hsuan Wei2015-08-06Released
Test_PubTator62Chih-Hsuan Wei2016-04-20Testing
NCBIDiseaseCorpus6.88 KRezarta Islamaj Doğan,Robert Leaman,Zhiyong LuChih-Hsuan Wei2015-08-06Released
Ab3P-abbreviations2.34 KSunghwan Sohn, Donald C Comeau, Won Kim and W John Wilburcomeau2016-07-29Beta
craft-sa-dev512 KUniversity of Colorado Anschutz Medical Campuscraft-st2019-03-25Released
craft-ca-core-dev62.3 KUniversity of Colorado Anschutz Medical Campuscraft-st2019-03-25Released
craft-ca-core-ex-dev94.3 KUniversity of Colorado Anschutz Medical Campuscraft-st2019-03-25Released
DLUT9314.57 KDLUT9312016-05-17Testing
test010Erika Asamizu2015-09-11Testing
Erin_test0ErinErinHJ_Kim2017-07-13Testing
bionlp-st-2016-SeeDev-dev61EstelleChaix2018-01-13Released
bionlp-st-2016-SeeDev-test184EstelleChaix2018-01-13Released
bionlp-st-2016-SeeDev-training35EstelleChaix2018-01-13Released
SPECIES8003.71 KEvangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensenevangelos2018-04-25Released
disease_gene_microbe_small536evangelos2018-01-13Testing