For each result, the F-measure as determined from the published gold-standards is given in brackets

<p><b>Copyright information:</b></p><p>Taken from "ProMiner: rule-based protein and gene entity recognition"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 1):S14-S14.</p><p>Published online 24 May 2005</p><p>PMCID:PMC1869006.</p><p></p> Details on this figure are provided in the section

Both candidates are wrong matches because the significant token "receptor" is present in the text

<p><b>Copyright information:</b></p><p>Taken from "ProMiner: rule-based protein and gene entity recognition"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 1):S14-S14.</p><p>Published online 24 May 2005</p><p>PMCID:PMC1869006.</p><p></p> Naive matching would accept both candidates

Concepts identified using the MS Ontology in the competency questions.

<p>Figure shows the concepts (in grey boxes) retrieved in the competency questions (search strategy) annotated by the MS Ontology and linked to other MS Ontology concepts, indicating the PMID of the abstract from PubMed and the type of interaction described in such abstract. A) references linking brain atrophy and CNS repair with remyelination in MS; B) references linking Myelin Oligodendrocyte Glycoprotein (MOG) to antibody-mediated demyelination; and C) references linking fingolimod tested as a drug for treatment of relapsing-remitting MS in phase 3 clinical trials</p

The MS Ontology.

<p>A) Basic formal ontology integration of MS Ontology; B) Extracted views of the MS Ontology showing the hierarchy of the concepts; C) Source documents for each category used for creating the ontology.</p

Comorbidities diagnosed in patients with MS identified in the EMR.

<p>Comorbidities diagnosed in patients with MS identified in the EMR.</p

Results of competency questions evaluation using MS Ontology compared to manual search on PubMed.

<p>Results are shown as the number of all retrieved documents and the “validated ones” based in manual review of the documents by the expert in order to ensure they were covering the topics of the competency questions. We define as the gold standard for calculating sensitivity, the expert search in PubMed using key words (related with AND) and the manual revision of the abstracts. In order to calculate ‘Sensitivity’ and ‘Specificity’ of MS Ontology based searches, true positives are defined as the number of ‘validated documents’ retrieved by a MS Ontology based search; false positive are the number of documents retrieved by MS Ontology based search but were not considered relevant in expert review and False negatives are the number of documents retrieved by ‘expert based searches’ in PubMed but were not retrieved by MS Ontology. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116718#pone.0116718.s001" target="_blank">S1 Methods</a> for details of the searches.</p><p>Results of competency questions evaluation using MS Ontology compared to manual search on PubMed.</p

Top 5-drug usage by patients with MS identified in the EMR.

<p>Top 5-drug usage by patients with MS identified in the EMR.</p