Difference between revisions of "The Comparative Toxicogenomics Database"

Revision as of 22:39, 1 October 2017

General Information

1. The Comparative Toxicogenomics Database
2. This database stores information on how environmental toxins affect our health.
   1. "It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships." About CTDbase A complete list of types of data includes:
      • Chemicals
      • Diseases
      • Genes
      • Chemical-Gene Interactions
      • References
      • Gene Ontology
      • Pathways
      • Organisms
      • Batch Query
      • Exposure Studies Query
      • Exposure Details Query
   2. The data is manually curated by a team of 5 database personnel. This database has secondary data integrated from the following resources:
      • BioGRID (3.4.151 release)
      • ChemIDplus® (as of August 18, 2017)
      • DrugBank (as of August 18, 2017)
      • GO (as of August 18, 2017)
      • KEGG (as of August 18, 2017)
      • MeSH® (2016 MeSH release)
      • NCBI Gene (as of August 18, 2017)
      • NCBI Taxonomy (as of August 18, 2017)
      • PubMed® (as of August 18, 2017)
      • Reactome (as of August 18, 2017)
3. CTD is a public database maintained by a team of 10 individuals, coming from North Carolina State University (NCSU), the Mount Desert Island Biological Laboratory (MDIBL), and remotely located biocurators. FAQ
4. CTD recieves funding from the National Institute of Environmental Health Sciences (NIEHS). Specific grant numbers can be found on the CTD's funding page.

Scientific Quality

General Utility

1. There are links to other databases...
2. not sure yet
   

   Description of image
3. Yes, downloading data is convenient. For example, one can download the table of diseases associated with gene W02A2.8 in several file formats. CSV, Excel, XML, and TSV files are all available to download, allowing users to choose whichever file format will work best with their favorite software. While making a specific query, data can also be downloaded in any of the following standard formats: TSV, CSV, JSON, or XML.
4. Yes, the database is very user-friendly, the database utilizes a broad to specific design. The user is able to click on legend icons for quick help. On the homepage, a clickable image navigates the user to the desired data category. It is very easy to query data, as it is a multi-step process that has "help" notifications the whole way. If a user is still confused, there are tutorial videos on how to navigate through the webpage.
5. The database is free to access for educational and research purposes only. Commercial use of this database is not allowed without prior written consent. Furthure information on access can be found on the CTD Legal Notices page.

Summary Judgement

Electronic Notebook

• On Friday, September 29, we met in the computer lab for 2.5 hours. we worked simultaneously on completing the questions for the week 5 journal questions as well as the outline for the in-class presentation. The questions were all answered based on our experience interacting with the database. Some answers were also found on the database's FAQ section.
• On Sunday, October 1, we met with the goal to finish this assignment page as well as the presentation.

Acknowledgements

References

• Davis AP, Grondin CJ, Johnson RJ, Sciaky D, King BL, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database: update 2017. Nucleic Acids Res. 2016 Sep 19;[Epub ahead of print]. Retrieved September 29, 2017.
• LMU BioDB 2017. (2017). Week 5. Retrieved September 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5.

Useful Links