Your assignment is to use natural language parsing techniques to "extract" knowledge from journal abstracts like the following:
AB - Transforming growth factor beta-1 (TGF-beta1), which is
present in lung tissue, has been suggested to play a role in
modulating vascular cell function in vivo. The action of
TGF-beta1 in vivo, especially at the local site of application
to connective tissue, is anabolic and leads to pulmonary
fibrosis and angiogenesis, strongly indicating that TGF-beta may
have practical applications in repair of tissue injury caused by
burns, trauma, or surgery. In the present study, we have used
cultured bovine pulmonary artery endothelial (BPAE) cells as a
model system. Expression of various proteins, including SPARC
(secreted protein acidic and rich in cysteines), type IV
procollagen and fibronectin (FN) was examined by radiolabeling
the cells with [3H]proline, immunoprecipitation with specific
antibodies, and Northern blot analyses by using specific cDNA
probes. Cultured cells were labeled with [3H]proline for 24 h in
either the absence or in the presence of TGF-beta1 (0-20
ng/ml). Incorporation of radioactivity was observed in a
concentration-dependent manner, maximal at 5 ng/ml. Northern
blot hybridization demonstrated that TGF-beta1 (5 ng/ml)
treatment of BPAE cells caused an increase in steady-state
levels
UI - 10753721
You should attempt to convert this knowledge into FOPL-like sentences such as the following.
Pay special attention to characterizations of ambient conditions (that the author may or may not make explicit!) which qualify the general statement of the fact.
We are collecting a list of relevant biomedical dictionaries and thesauri
D. Swanson's search for "implicit knowledge" is one inspiration. For a quick gloss, see: Finding Out About, Sect. 6.5.3
Ontologies especially designed for biological concepts include EcoCYC, RiboWeb (Russ Altman) and (a recent effort) TAMBIS.
Obviously, attempting to bring structure to these unstructured data sources is likely to mediated using XML resources. A couple emerging standards especially designed for biomedical content are: BSML and BioML