BioCreative MetaServer Service

• A BioCreative MetaServer Service is a metaserver for text mining and information extraction in BioSciences.
• AKA: BCMS.
  • …
• Example(s):
  • BioCreative I (2004)
  • BioCreative II (2006)
  • BioCreative III (2010).
  • …
• Counter-Examples(s):
  • BioText Search Engine.
  • BIOSIS
  • PubMed.
  • GoPubMed.
  • OVID.
  • EMBASE.
  • MEDLINE.
  • HubMed.
• See: Bioinformatics, Biomedicine, Search Engine, Text Mining MetaServer, Meta-Search-Engine, DNS MetaServer, Gene Mention Recognition System, Gene Mention Normalization System, Gene Ontology.

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References

2017a

• (BioCreative) ⇒ http://www.biocreative.org/about/background/description/ Retrieved on 2017-05-27
  • The BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) challenge evaluation consists of a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain.

The organization of BioCreAtIvE was motivated by the increasing number of groups working in the area of text mining. However, despite increased activity in this area, there were no common standards or shared evaluation criteria to enable comparison among the different approaches. The various groups were addressing different problems, often using private data sets, and as a result, it was impossible to determine how good the existing systems were, whether they would scale to real applications, and what performance could be expected(...)

2017b

• (Wikipedia, 2017) ⇒ https://en.wikipedia.org/wiki/Metaserver#Example_MetaServer_projects Retrieved:2017-5-28.
  • Typical, widespread implementations of MetaServers are:
    • Meta-Search-Engines.
    • DNS MetaServers.
    • Protein Structure and Function Prediction Gateways.
    • Computer Game MetaServers.
    • Text Mining MetaServers (e.g. BioCreative Metaserver - BCMS)

2008

• (Leitner et al., 2008) ⇒ Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu,Richard Tzong-Han Tsai, Hsi-Chuan Hung William W Lau, Calvin A Johnson, Rune Sætre, Kazuhiro Yoshida, Yan Hua Chen, Sun Kim, Soo-Yong Shin, Byoung-Tak Zhang, William A. Baumgartner Jr, Lawrence Hunter, Barry Haddow, Michael Matthews, Xinglong Wang, Patrick Ruch, Frédéric Ehrler, Arzucan Özgür, Güneş Erkan, Dragomir Radev, Michael Krauthammer, ThaiBinh Luong, Robert Hoffmann, Chris Sander, and Alfonso Valencia. (2008). “Introducing Meta-Services for Biomedical Information Extraction.” In: Genome Biology 2008, 9(Suppl 2):S6
  • Topics: Gene Mention Recognition System, Gene Mention Normalization System, PubMed, Uniprot, BMCS, BioCreate Meta-Services.
  • ABSTRACT: We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/ webcite). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.

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