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User 'evangelos'

Projects

NameTDescription# Ann.Updated atStatus
1-4 / 4
SPECIES800_autotaggedThis project comprises the SPECIES800 corpus documents automatically annotated by the Jensenlab tagger. Annotated entity types are: Genes/proteins from the mentioned organisms (and any human ones) PubChem Compound identifiers NCBI Taxonomy entries Gene Ontology cellular component terms BRENDA Tissue Ontology terms Disease Ontology terms Environment Ontology terms The SPECIES 800 (S800) comprises 800 PubMed abstracts. In its original form species mentions were manually 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.0065390. The manually annotated corpus is also available as a PubAnnotation project (see here). 02015-11-20Testing
disease_ontology_term_microbe52018-04-25Developing
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 K2018-04-25Released
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-mentions5362018-01-13Testing

Automatic annotators

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Editors

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