Table 5

Features Used for Ranking

TestFile

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M37','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M37">View MathML</a>

EntityType

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M38','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M38">View MathML</a>

String

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M39','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M39">View MathML</a>

GeneSyn

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M40','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M40">View MathML</a>

Labels

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M41','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M41">View MathML</a>

String

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M37','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M37">View MathML</a>

TestFile

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M42','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M42">View MathML</a>

GeneId

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M43','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M43">View MathML</a>

TERM

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M44','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M44">View MathML</a>

TrainFile

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M45','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M45">View MathML</a>

Labels

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M46','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M46">View MathML</a>

Labels

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M47','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M47">View MathML</a>

TrainFile

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M48','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M48">View MathML</a>

String

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M49','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M49">View MathML</a>

TestFile

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M50','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M50">View MathML</a>

TestFile

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M48','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M48">View MathML</a>

String

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M51','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M51">View MathML</a>

String

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M52','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M52">View MathML</a>

GeneSyn

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M37','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M37">View MathML</a>

TrainFile

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M37','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M37">View MathML</a>

GeneId

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M53','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M53">View MathML</a>

String

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M54','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M54">View MathML</a>

Labels

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M55','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M55">View MathML</a>

EntityType

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M56','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M56">View MathML</a>


The final set of features used by learning system, in the format

<a onClick="popup('http://www.biomedcentral.com/1471-2105/7/440/mathml/M57','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2105/7/440/mathml/M57">View MathML</a>

, where t is a node type, and ℓ is an edge label. The edge labels likelyProtNER and possibleProtNER are shortcut representing the baseline NER methods. The edge labels likelyProt2syn and possibleProt2syn are links between extracted protein names and softTFIDF-similar protein synonyms.

Cohen and Minkov BMC Bioinformatics 2006 7:440   doi:10.1186/1471-2105-7-440

Open Data