• LifeWatch ERIC Metadata Catalogue
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Literature Mining virtual Lab

Biodiversity literature and data constitute a vast public resource open to mining and knowledge extraction.

Associating organisms to key features of their life, for example the environment in which they live, the way feed, their breeding habits, is cornerstone in explaining biodiversity patterns and informing ecological decisions.

The Literature Mining virtual Lab (LM-vLab) aims at the automatic extraction of species - traits associations from the literature.

The Literature Mining vLab is a collection of: applications (EXTRACT annotation tool, ENVIRONMENTS and SPECIES/ORGANISMS taggers) and analysis datasets ("ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life"

Simple

Identification

Date ( Publication )
2021
Status
Completed
Author
  -
 
OnLine resource
Link to the VRE ( WWW:LINK-1.0-http--link )
OnLine resource
Info page ( WWW:LINK-1.0-http--link )
Individual Name
Evangelos Pafilis
Address
IMBBC, LifeWatch Greece, HCMR
E-Mail
pafilis[at]hcmr.gr
Service Name
Semantic annotation
Service Description
The tools can be used for semantic annotation (e.g. tagging of organism names, and environment types mentioned in a piece of text).
Publications about this VRE
Pafilis, E., Frankild, S. P., Fanini, L., Faulwetter, S., Pavloudi, C., et al. (2013). The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. PLoS ONE 8(6): e65390
Publications about this VRE
Pafilis, E., Buttigieg, P. L., Ferrell, B., et al. (2016). EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database, baw005
Publications about this VRE
Pafilis, E., Frankild, S. P., Schnetzer, J., et al (2015). ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. Bioinformatics (btv045)
 

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