Table 5

Roadmap for refactoring corpora. The list of corpora came from [32] and [33], where there are links to the corpora. Column headings indicate the steps that corpora may need to undergo to be refactored; those corpora that would require that step are noted with a dot. The heading "get original" means the original text needs to be retrieved. "Detect spans" means the corpus is a metadata corpus so spans of entities need to be detected. "Alt. search" means techniques other than exact-match searching must be used.

get original
 detect spans
 alt. search
Arabidopsis Thaliana Circadian Rhythms [34]
 •

Bio1 [35]
 •

BioCreative 2004 Task 1A [28]
 •
•
BioCreative 2004 Task 1B [36]
•
 •
BioCreative 2004 Task 2 [37]
•
 •
BioCreative 2006 Task GM [38]


BioCreative 2006 Task GN [39]


BioCreative 2006 Task IPS/IMS [40]
•
 •
BioCreative 2006 Task ISS [40]
•
BioInfer [41]


BioText: Recognizing Abbreviation Defintions [42]


BioText: Protein-Protein Interaction Data [43]
 •
•
BioText: Relations between Disease/Treatment Entities [44]
 •

Brown-Genia Treebank [45]
 •

DepGenia [46]
 •

DIPPPI [47]
•
 •
EDGAR [48]
 •
 •
GENIA [49, 50]
 •

FetchProt [51]


Human Gene ID-Serve
 •

IEPA [52]
 •
 •
ImmunoTome
 •

iProLink [53]


Medstract [54, 55]


MedTag [7]


OHSUMED [56, 57]
 •
 •
 •
PASBio [58]
•
PASTA [59]


PathBinder [60]


PennBioIE [12]


PICorpus


ProSpecTome [61]
 •
 •
PDG [9]
 •
 •
 •
Texas [62]
 •
•
TREC Genomics 2004 Categorization Task [63]
•
 •
TREC Genomics 2005 Categorization Task [64]
•
 •
TREC Gemonics 2006 IR Task [65]
•
 •
TREC Genomics 2007 IR Task [65]
•
 •
Wisconsin [66]
 •
 •
 •
WSD [67]


Yapex [68, 69]
 •

Johnson et al. Journal of Biomedical Discovery and Collaboration 2007 2:4   doi:10.1186/1747-5333-2-4