Literature mining for the biologist

From information retrieval to biological discovery

Lars Juhl Jensen, Jasmin Saric and Peer Bork

Network figure

To facilitate detailed inspection of the protein network shown in Figures 3 and S1, we here make available a zoomable version of the network. The names of all proteins are written with a tiny font within the nodes of the network and are linked with the STRING web server.

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Bibliography

Many more papers than can possibly be cited in a single review have been published on the topics related to biological literature mining. We thus here make available an extended bibliography sorted by topic.

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Web resources

• Web-based applications
• Information retrieval (IR)
• E-BioSci
• EBIMed
• Google Scholar
• GoPubMed
• MedMiner
• PubMed
• PubFinder
• Textpresso
• XplorMed
• Entity recognition (ER)
• iHOP
• Information extraction (IE)
• iProLINK
• JournalMine
• PreBIND
• PubGene
• Text mining
• ARROWSMITH
• Integration
• BITOLA
• G2D
• ProLinks
• STRING
• Text collections
• Full text corpora
• HighWire Press
• PubMed Central
• Tagged corpora
• FetchProt
• GENETAG
• GENIA
• PennBioIE
• Yapex
• IE modules
• Entity taggers
• ABNER
• GAPSCORE
• Part-of-speech taggers
• Brill Tagger
• TNT Tagger
• TreeTagger
• Parsers
• CASS
• Collins Parser
• Stanford Parser

Maintained by Lars Juhl Jensen and Jasmin Saric
Last modified 28 October 2005