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User 'Yue Wang'

Projects

NameT Description# Ann.Updated atStatus
1-10 / 15 show all
jnlpba-st-trainingThe training data used in the task came from the GENIA version 3.02 corpus, This was formed from a controlled search on MEDLINE using the MeSH terms "human", "blood cells" and "transcription factors". From this search, 1,999 abstracts were selected and hand annotated according to a small taxonomy of 48 classes based on a chemical classification. Among the classes, 36 terminal classes were used to annotate the GENIA corpus. For the shared task only the classes protein, DNA, RNA, cell line and cell type were used. The first three incorporate several subclasses from the original taxonomy while the last two are interesting in order to make the task realistic for post-processing by a potential template filling application. The publication year of the training set ranges over 1990~1999.51.3 K2017-04-14Released
AnEM_full-texts250 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.6892016-07-27Uploading
AnEM_abstracts250 documents selected randomly from citation abstracts 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_full-texts, it is probably the largest manually annotated corpus on anatomical entities.1.95 K2016-06-07Released
bionlp-st-cg-2013-trainingThe training dataset from the cancer genetics task in the BioNLP Shared Task 2013. Composed of anatomical and molecular entities.10.9 K2016-12-06Released
AIMedThe AIMed corpus is one of the most widely used corpora for protein-protein interaction extraction. The protein annotations are either parts of the protein interaction annotations, or are uninvolved in any protein interaction annotation. Publication: http://www.cs.utexas.edu/~ml/papers/bionlp-aimed-04.pdf4.04 K2017-04-14Testing
PennBioIEThe PennBioIE corpus (0.9) covers two domains of biomedical knowledge. One is the inhibition of the cytochrome P450 family of enzymes (CYP450 or CYP for short) , and the other domain is the molecular genetics of dance (oncology or onco for short).23.9 K2016-12-06Released
bionlp-st-id-2011-trainingThe 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 K2017-04-18Released
bionlp-st-pc-2013-trainingThe 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 K2017-08-28Released
bionlp-st-bb3-2016-trainingEntity (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.1.29 K2017-05-22Released
PIR-corpus1The Protein Information Resource (PIR) is not biased towards any particular biomedical domain, and is expected to provide more diverse protein names in a given sample size. Annotation category: protein, compound-protein, acronym.4.44 K2016-11-14Released

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