The Comparative Toxicogenomics Database

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General Information

  1. The database we chose is titled The Comparative Toxicogenomics Database, or CTD for short.
  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.

      This figure shows three pathways that one can take while browsing in order to get to the page with data on Ascorbic Acid. The pathway highlighted in the red box is the one we took to Ascorbic Acid.
  2. Browsing the data isn't particularly difficult, but neither is it particularly easy. The browsing experience really depends on the type of data you are looking for. There are several categories of data, but within each category the browsing capability changes.
    • In the gene category, there is no way to filter the data; genes are simply listed alphabetically. Finding a gene this way is quite tedious due to the sheer amount of data. To find data, it is much easier to perform 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.
    • For information on exposure studies, no browsing is available.
    • Data browsing is only convenient for chemicals or diseases. The database provides a navigational list of chemical/disease categories that become more narrow with each click. For example, I was able to find information on different variations of Ascorbic Acid quite easily, since I knew it was an acidic sugar.
      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.

Summary Judgement

  1. As an inexperienced user who has very little knowledge about comparative toxicogenomics, I would not recommend this database to them. I believe that there should be some knowledge about the field beforehand before utilizing the database. For me personally, I do not know how I would use this information for my personal benefit other than appreciation for the field.
  2. The Comparative Toxicogenomic Database is quite clearly a database made by professionals, for professionals. The staff consists of several post doctoral curators, and the information contained within the database is not useful for many users outside of this specific field. Despite this, it is obvious that the database is quite useful for the task it was designed to do.

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. We first figured out which database to use - we wanted to choose something interesting yet different. Katie expressed some interest in toxicology, so we agreed on the Comparative Toxicogenomics Database, or CTD for short. we ended up completing about half of the assignment.
  • On Sunday, October 1, we met with the goal to finish this assignment page as well as the presentation. We were able to complete most of the assignement. as we just had to tweak and fine tune some of the specifications.
  • Overall, we learned about how CTD goes about curating, storing, and organizing their data. It seems like CTD was aware of the complexity of the field, so they tried to make it as user-friendly as they could, without changing the primary focus for the database. CTD has around 35 million manually curated data that has been well preserved and readily available for public use.
  • While not part of the assignment, we found information about the technology that runs CTD. We thought that it was really interesting that most of the software and services used by the database are open source. This is another example of why supporting open source computing is important; it allows projects like CTD become reality without as many prohibitive costs.

Link to PDF of Presentation Slides

Media:BioDB_CTD.pdf

Acknowledgements

  • Zach and Katie would like to thank each other for being good homework partners. We met in the afternoon on Friday and Sunday to write this wiki page and our presentation slides. We also plan on meeting Monday to rehearse our presentation.
  • While we worked with the people noted above, this journal entry was completed by Zach and Katie and not copied from another source.

Kwrigh35 (talk) 17:11, 1 October 2017 (PDT)
Zvanysse (talk) 17:12, 1 October 2017 (PDT)

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
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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
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Zvanysse

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

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

Individual Assignments

Zvanysse Week 1 | Zvanysse Week 2 | Zvanysse Week 3 | Zvanysse Week 4 | Zvanysse Week 5 | Zvanysse Week 6 | Zvanysse Week 7 | Zvanysse Week 8 | Zvanysse Week 9 | Zvanysse Week 10 | Zvanysse Week 11 | Zvanysse Week 12 | Zvanysse Week 14 | Zvanysse Week 15

Shared Journals

Zvanysse Week 1 Journal | Zvanysse Week 2 Journal | Zvanysse Week 3 Journal | Zvanysse Week 4 Journal | Zvanysse Week 5 Journal | Zvanysse Week 6 Journal | Zvanysse Week 7 Journal | Zvanysse Week 8 Journal | Zvanysse Week 9 Journal | Zvanysse Week 10 Journal | Zvanysse Week 11 Journal | Zvanysse Week 12 Journal | Zvanysse Week 14 Journal

Retrieved from "https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php?title=The_Comparative_Toxicogenomics_Database&oldid=2338"