The Comparative Toxicogenomics Database

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

1. There are currently 34,572,272 unique records held by the CTD.
   • CTD proudly claims the integrity of secondary sources harvested by manual curation.
   • The CTD does not claim for absolute coverage of toxicogenomic information - as the data grows faster than what the curators' can handle.
2. The CTD has no specific species, as CTD strives to log and curate all toxicogenomic data.
3. The CTD's data is relevant in order to analyze the affects between the following categories: Chemicals, Pathways, Diseases, Exposures, Genes, and Gene Ontology.
4. The information provided by CTD is relevant because toxicogenomics help us to understand, and hopefully cure, diseases. As for the data logistics themselves, CTD is the only comparative toxicogenomics database - however the primary source data may be found elsewhere. CTD claims to be celebrating 10 years, however the domain was instantiated online on November 2, 2011. The CTD tries to update information on a monthly basis. Sometimes they are a little early, or late, as the last update was August 24th.

General Utility

1. Links to the following databases can be found on the CTD Data Status page:
   • 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)

     Links to PubMed are also sprinkled throughout the database, particularly as links to the specific scientific article page that a piece of datum comes from.

2. Browsing the data isn't particularly difficult, but neither is it particularly easy. One of the reasons why it is difficult to browse CTD is because of the sheer amount of data it contains. There are very few ways to filter the data when browsing. It is much easier to find data by performing a broad search with a few well thought out parameters, and then browse the results. Conducting a search that casts a wide net makes the data much more manageable.
   

   Links to download data spreadsheets are at the bottom of each page. In this image they are highlighted by a red box.
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.

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.

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

Category	Links
Interwiki	Main Page   Katie Wright   Course schedule Lights, Camera, InterACTION!
Katie Wright Weekly Assignment	Week 2   Week 3   Week 4  Week 5  Week 6  Week 7  Week 8  Week 9🎃  Week 10  Week 11  Week 12  Week 13  Week 14  Week 15
Weekly Assignment Instructions	Week 1   Week 2   Week 3   Week 4   Week 5   Week 6   Week 7   Week 8   Week 9   Week 10   Week 11   Week 12   Week 14   Week 15
Class Journals	Week 1   Week 2   Week 3   Week 4   Week 5   Week 6   Week 7   Week 8   Week 9   Week 10   Week 11   Week 12   Week 13   Week 14