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NameTDescription# Ann. AuthorMaintainerUpdated_atStatus

121-140 / 316 show all
bionlp-ost-19-BB-norm-dev 1.33 Kldeleger2023-11-29Developing
bionlp-st-bb3-2016-training Entity (bacteria, habitats and geographical places) annotation to the training dataset of the BioNLP-ST 2016 BB task. For more information, please refer to bionlp-st-bb3-2016-development and bionlp-st-bb3-2016-test. Bacteria Bacteria entities are annotated as contiguous spans of text that contains a full unambiguous prokaryote taxon name, the type label is Bacteria. The Bacteria type is a taxon, at any taxonomic level from phylum (Eubacteria) to strain. The category that the text entities have to be assigned to is the most specific and unique category of the NCBI taxonomy resource. In case a given strain, or a group of strains is not referenced by NCBI, it is assigned with the closest taxid in the taxonomy. Habitat Habitat entities are annotated as spans of text that contains a complete mention of a potential habitat for bacteria, the type label is Habitat. Habitat entities are assigned one or several concepts from the habitat subpart of the OntoBiotope ontology. The assigned concepts are as specific as possible. OntoBiotope defines most relevant microorganism habitats from all areas considered by microbial ecology (hosts, natural environment, anthropized environments, food, medical, etc.). Habitat entities are rarely referential entities, they are usually noun phrases including properties and modifiers. There are rare cases of habitats referred with adjectives or verbs. The spans are generally contiguous but some of them are discontinuous in order to cope with conjunctions. Geographical Geographical entities are geographical and organization places denoted by official names.1.28 KINRAYue Wang2023-11-29Released
MicrobeTaxon 1.23 KYo Shidahara2023-11-26Testing
SCAI-Test A small corpus for the evaluation of dictionaries containing chemical entities. Publication: http://www.scai.fraunhofer.de/fileadmin/images/bio/data_mining/paper/kolarik2008.pdf Original source: https://www.scai.fraunhofer.de/en/business-research-areas/bioinformatics/downloads/corpora-for-chemical-entity-recognition.html1.21 KCALBC ProjectYue Wang2023-11-28Released
CyanoBase Cyanobacteria are prokaryotic organisms that have served as important model organisms for studying oxygenic photosynthesis and have played a significant role in the Earthfs history as primary producers of atmospheric oxygen. Publication: http://www.aclweb.org/anthology/W12-24301.1 KKazusa DNA Research Institute and Database Center for Life Science (DBCLS)Yue Wang2023-11-26Released
Glycobiology-GlycanName 946Toshihide Shikanaishikanai2023-11-27Testing
WikiPainGoldStandard Wiki-pain contains molecular interactions that are relevant to pain.878Daniel Jamiesonnikolamilosevic2023-11-28Developing
bionlp-st-ge-2016-coref Coreference annotation to the benchmark data set (reference and test) of BioNLP-ST 2016 GE task. For detailed information, please refer to the benchmark reference data set (bionlp-st-ge-2016-reference) and benchmark test data set (bionlp-st-ge-2016-test).853DBCLSJin-Dong Kim2023-11-28Released
AnEM_full-texts 250 documents selected randomly from full-text papers Entity types: organism subdivision, anatomical system, organ, multi-tissue structure, tissue, cell, developing anatomical structure, cellular component, organism substance, immaterial anatomical entity and pathological formation Together with AnEM_abstracts, it is probably the largest manually annotated corpus on anatomical entities.687NaCTeMYue Wang2023-11-29Uploading
Trait_curation150831 620Sachiko_ShirasawaSachiko Shirasawa2023-11-29Testing
Goldhamster2_CellLineAnn 618zebet2023-11-29Developing
ENG_NER_NEL_CONSENSUS 607dpavot2023-11-28Developing
Wangshuguang HZAU_bioinformatics_competition603wangshuguangwangshuguang2023-11-29Released
ENG_NER_NEL_pruas 582Pedro Ruaspruas_182023-11-30Developing
Test20200205 553BLAH6-Tweets2023-11-29Testing
LitCovid-manual 540Jin-Dong Kim2023-11-30Developing
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
FA_PR25 FirstAuthor Protein Ontology 25 entries512AikoHIRAKI2023-11-29Developing
test_lasige 494Jin-Dong Kim2023-12-02Testing
Trait curation Project for trait curation in PGDBj479Sachiko ShirasawaSachiko Shirasawa2023-11-24Testing
NameT# Ann. AuthorMaintainerUpdated_atStatus

121-140 / 316 show all
bionlp-ost-19-BB-norm-dev 1.33 Kldeleger2023-11-29Developing
bionlp-st-bb3-2016-training 1.28 KINRAYue Wang2023-11-29Released
MicrobeTaxon 1.23 KYo Shidahara2023-11-26Testing
SCAI-Test 1.21 KCALBC ProjectYue Wang2023-11-28Released
CyanoBase 1.1 KKazusa DNA Research Institute and Database Center for Life Science (DBCLS)Yue Wang2023-11-26Released
Glycobiology-GlycanName 946Toshihide Shikanaishikanai2023-11-27Testing
WikiPainGoldStandard 878Daniel Jamiesonnikolamilosevic2023-11-28Developing
bionlp-st-ge-2016-coref 853DBCLSJin-Dong Kim2023-11-28Released
AnEM_full-texts 687NaCTeMYue Wang2023-11-29Uploading
Trait_curation150831 620Sachiko_ShirasawaSachiko Shirasawa2023-11-29Testing
Goldhamster2_CellLineAnn 618zebet2023-11-29Developing
ENG_NER_NEL_CONSENSUS 607dpavot2023-11-28Developing
Wangshuguang 603wangshuguangwangshuguang2023-11-29Released
ENG_NER_NEL_pruas 582Pedro Ruaspruas_182023-11-30Developing
Test20200205 553BLAH6-Tweets2023-11-29Testing
LitCovid-manual 540Jin-Dong Kim2023-11-30Developing
disease_gene_microbe_small 536evangelos2023-11-27Testing
FA_PR25 512AikoHIRAKI2023-11-29Developing
test_lasige 494Jin-Dong Kim2023-12-02Testing
Trait curation 479Sachiko ShirasawaSachiko Shirasawa2023-11-24Testing