Measuring Expert Performance at Manually Classifying Domain Entities under Upper Ontology Classes: Data and Scripts

Dataset containing the analysis for the journal paper submission "Measuring Expert Performance at Manually Classifying Domain Entities under Upper Ontology Classes".<div><br></div><div>The output generated by the script can be seen here:</div><div>http://rpubs.com/matentzn/upperontologyclassification<br></div

Additional file 2: of Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

The list of journals mined for disease-phenotype assocations. (PDF 13 kb

Additional file 1: of Linking rare and common disease: mapping clinical disease-phenotypes to ontologies in therapeutic target validation

URLs to the supplementary downloadable result files for text mining results (IBD, Autoimmunity, Skeletal disorders, and Metabolism disorders). (PDF 18 kb

Partial high-level structure of OBI classes.

<p>OBI classes are shown in blue. Classes imported from BFO, IAO and other external ontologies are shown in orange, purple and dark red, respectively. Some example subclasses, such as <i>device</i> and <i>processed specimen</i> are included to illustrate the use of the class <i>processed material</i>.</p

Measuring glucose concentration in blood.

<p>The large boxes represent instances of processes and their participants. The <i>collecting specimen from organism</i> process takes place first. In this process, a <i>syringe</i> is used to draw blood from the mouse. At the end of this process a tube contains the <i>blood specimen</i>. In a second process, this specimen is used in an <i>analyte assay</i>, which measures the concentration of glucose in the blood. A <i>glucometer</i> is used to make this measurement. The <i>analyte role</i> inheres in the <i>glucose molecules</i> scattered throughout the <i>blood specimen</i>. This <i>planned process</i> achieves the <i>analyte measurement objective</i>.</p

Eagle-i record-level citation widget.

<p>Eagle-i record-level citation widget.</p

Record-level versioning and release-level versioning.

<p>Record-level versioning and release-level versioning.</p

A summary of the 10 recommendations and their direct or indirect impact on different kinds of identifier roles.

<p>A summary of the 10 recommendations and their direct or indirect impact on different kinds of identifier roles.</p

Anatomy of a web-based identifier.

<p>An example of an exemplary unique resource identifier (URI) is below; it is comprised of American Standard Code for Information Interchange (ASCII) characters and follows a pattern that starts with a fixed set of characters (URI pattern). That URI pattern is followed by a local identifier (local ID)—an identifier which, by itself, is only guaranteed to be locally unique within the database or source. A local ID is sometimes referred to as an “accession.” Note this figure illustrates the simplest representation; nuances regarding versioning are covered in Lesson 6 and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2001414#pbio.2001414.g005" target="_blank">Fig 5</a>.</p

Desirable characteristics for database identifiers in the life sciences.

<p>Desirable characteristics for database identifiers in the life sciences.</p