For the last 30 years astronomers have been grappling with issues pertaining to the elemental abundance measurements of star-forming regions, since these nebulae are key to probing the chemical composition of distant galaxies. Pressing problems remain, however, in our interpretation and understanding of the emission line spectra of Galactic and extragalactic regions of massive star formation. The most important of these is the so-called abundance anomaly problem which casts considerable uncertainty on our knowledge of the composition of the local, and hence most easily measurable, regions and thus has repercussions for chemical enrichment in the more distant Universe. This proposal has the ambitious, but realistic, goal to resolve this problem in the context of an innovative study of protoplanetary disks and young stellar objects in star-forming regions. Using multi-waveband observations from the latest ground- and spaced-based techniques, and advanced numerical models, the tomography of the targets will be undertaken and new diagnostics of their physical properties and chemical element composition will be developed. Such a detailed study is essential if the long-standing ambiguity surrounding established methods in deriving chemical abundances out to distant galaxies is to be removed, and it will promote a new understanding of protoplanetary disks and the small-scale structure of the interstellar medium. The proposed research will provide first-class training to an experienced researcher in advanced observational and modelling methods, and contribute to the solution of one of the most debated problems of nebular astrophysics. In the process, it will boost his career towards scientific independence, maturity, and excellence.