Term Paper: Database Presentation

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[. . .] " (Mocellin, et al., 2010, p.1) The user can query the database for the following:

(1) To provide both basic researchers and clinical investigators with an unprecedented synopsis of the available scientific literature regarding the targeted therapy of melanoma (Mocellin, et al., 2010, p.1)

(2) To obtain summaries of the current evidence about the relationship between single molecules (or set of molecules) and the efficacy (or toxicity) of a given therapeutic agent (or set of therapeutic agents); summaries regarding the synergisms between drugs (conventional and/or targeted drugs) can also be obtained (Mocellin, et al., 2010, p.1); and (3) To match the patient (cancer) molecular profile with the available scientific evidence about the targeted therapy of melanoma, thus developing a drug ranking system for the personalized treatment of melanoma. (Mocellin, et al., 2010, p.1)

Mocellin et al. states that the information collected in the TTD makes provision of "…an overall picture of the data produced by the scientific community with regard to anti-melanoma targeted therapy, which are currently scattered in thousands of individual articles published in hundreds of journals often not open-access. Even more importantly, the computational analysis of the TTD data may prove useful to promote both the preclinical and clinical development of patient-tailored therapy based on the comprehensive (instead of piecewise) use of the available evidence." (Mocellin, et al., 2010, p.1)

The sources of information input in the TTD include: (1) PubMed; (2) Medline; (3) Embase; (4) Cancerlit; and (5) Cochrane databases. (Mocellin, et al., 2010, p.1) The database contains 15 columns including the identifying number, the source, the molecule, the molecule's alias, the conditions of the molecule, the modifier, the modifier alias, the relationship between the molecule and the corresponding treatment; the drug, the drug alias, the model (there are seven of these), the hypothesis, the cases, the reference and notes.

The TTD has as its goal enabling investigators to locate targeted therapy related information that is organized "in a standardized and computationally oriented fashion. For example the following illustration shows the example of evidence synopsis regarding the targeted therapy of melanoma as obtained by searching the Targeted Therapy Database.

Figure 1

Source: Mocellin, et al. (2010)

The work of Zhu et al. (2010) reports "TTD data can be accessed by keyword or customized search. Customized search fields include target name, drug name, disease indication, target biochemical class, target species, drug therapeutic class, and drug mode of action. Further information about each target can be accessed via crosslink to UniProtKBSwissProt, PDB, KEGG, OMID and Brenda database. Further drug information can be accessed via crosslink to PubChem, DrugBank, SuperDrug and ChEBI. Related target or drug entries can be recursively searched by clicking a disease or drug name. Similarity targets of an input protein sequence in FASTA format can be searched by using the BLAST sequence alignment tool. Similarity drugs of an input drug structure can be searched by using molecular descriptor-based Tanimoto similarity searching method. Target and drug entries are assigned standardized TTD IDs for easy identification, analysis and linkage to other related databases. The whole TTD data, target sequences along with Swissprot and Entrez gene IDs, and drug structures can be downloaded via the download link. A separate downloadable file contains the list of TTD drug ID, drug name and the corresponding IDs in other cross-matching databases PubChem, DrugBank, SuperDrug and ChEBI. The corresponding HGNC name and Swissprot and Entrez gene ID of each target is provided in the target page. The SMILES and InCHI of each drug is provided in the drug page." (2010, p.1)

Summary and Conclusion

The aim of the Targeted Therapy Database is to allow researchers to access a summary of the evidence available on any given subject, which is important from a therapeutic perspective in understanding the overall effect of a therapy in relation to the possible harm of any given treatment.


Zhu, Feng, et al. (2010) Update of TTD: Therapeutic Target Database. Nucleic Acids Res 2010, Jan; 38. Retrieved from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808971/

Mocellin, S. (2010) Targeted Therapy Database (TTD): A Model to Match Patient's Molecular Profile with Current Knowledge on Cancer Biology. PLoS. Retrieved from: http://www.plosone.org/article/citationList.action;jsessionid=9668016174E6CACB8CFBBB1BD64BC81B?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.0011965

Chen, ZL and Chen, YZ (2002) TTD: Therapeutic Target Database. Nucl. Acids Res. 39 (1). Retrieved from: http://nar.oxfordjournals.org/content/30/1/412.full [END OF PREVIEW]

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