CancerTracer Review

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Purpose

The purpose of this assignment is to familiarize ourselves with databases and develop skills to successfully navigate and decipher pertinence and validity of the presented information. CancerTracer is the specific database being reviewed based on its content, organization, and maintenance.

Database Evaluation

General information about the database

  1. What is the name of the database? (link to the home page)
  2. What type (or types) of database is it?
    • Cancer Tracer is a data base that collects tumor heterogeneity. They split their data into intratumor and intertumor. The intratumor analyzes subclones within a single tumor or metastatic lesion. The intertumor data analyzes the subclones from multiple tumors in the same patient. The data comes from other publicly published studies and is consistently manually curated by a human staff. They commonly use the analogy of a tree when describing how their data is like the branches that lead scientists to the trunk (cancer therapeutics and advancements in treatments).
    • CancerTracer Homepage
  3. What individual or organization maintains the database?
    • The Cali Lab of the College of Life Sciences at Sichuan University in China runs Cancer Tracer. The database is available for public use and can easily be downloaded from their website.
    • CancerTracer Contact page
  4. What is their funding source(s)?

Scientific quality of the database

  1. Does the content appear to completely cover its content domain?
    • Cancer Tracer has samples from over 6000 tumors that came directly from 1548 patients (at the time of the paper publication).
    • The paper written about the data base elaborate on the specifics of the data. It includes sample from 45 different cancer types and was taken from 145 public studies. The paper also points out that they have over 1000 samples of the TP53 gene which is the mostly commonly mutated in all cancers.
  2. What species are covered in the database? (If it is a very long list, summarize.)
    • There are 45 different types of cancer/tumors that are in the data base but some of the major ones are lung cancer, colorectal cancer, glioma cancer, esophageal cancer, and breast cancer. All these types range from eight percent of sample in the database to eighteen percent. The forty other types of cancer take up the remaining 31.1 percent of samples.
  3. Is the database content useful? I.e., what biological questions can it be used to answer?
    • The database is primarily used to track cancers that have abnormal mutations in their genome. It is certainly a niche area of study, but if you need information on what type of cancers modify their sequence as they progress/move throughout the body then Cancer Tracer is a great resource.
    • CancerTracer Homepage
  4. Is the database content timely?
    • Given that cancer is one of the leading causes of death in America and the world, any research or data on cancer is very useful. While this data may not be applicable to too many types of cancer (most of its data is on just five types) people still suffer from those types and thus there is a need for this data.
    • As far as I am aware there is no other database that organizes the data like Cancer Tracer. They mention in the paper that all their data does come from other public studies, but the organization based on inter versus intra is something that is new.
    • The database was first published in November of 2019 and has not been updated since.

General utility of the database to the scientific community

    1. Are there links to other databases? Which ones?
      • There were database links provided with results on specific genes within the CancerTracer database. Suppose the user was only interested in genes of known cancer genes, further information was linked to the COSMIC database. Another example would be when limiting results to relation between specific mutations, the CancerTracer database provides suggested databases with the related information such as DGIdb, PreMedKB, or Nature Score. As the information of this database is a compilation of many databases, it provides links to all original literature varying from multiple database sources including PubMed, MethCNA, etc CancerTracer Related Resource, CancerTracer Tutorial
    2. Is it convenient to browse the data?
      • The webpage is extremely user-friendly offering clear sections to input data and concise pages to access certain features. Additionally the CancerTracer provides a tutorial page that provides examples and simple directions explaining how to navigate the database CancerTracer Tutorial
    3. Is it convenient to download the data? In what file formats are the data provided? What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)? Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
      • CancerTracer provides a separate page to access and download all pertaining information from their webpage making it extremely convenient. All files are provided in an approved standard in .txt file extension CancerTracer Download Page
    4. Evaluate the “user-friendliness” of the database: can a naïve user quickly navigate the website and gather useful information?
      • The page is extremely user friendly providing a great tutorial page as well as a very simple yet explanatory introduction of the page. There are no complex inputs required and the data is easily accessible in the interactive pages, including well explained graphs and headers. making it easy to gather information CancerTracer Homepage
    5. Is the website well-organized?
      • Yes the page is separated into 6 distinct pages and provides simple subsections on each page. It separates Intertumor and Intratumor data allowing specification when comparing trees CancerTracer Homepage
    6. Does it have a help section or tutorial?
      • It provides a tutorial section with separate sections regarding each page on the database CancerTracer Tutorial
    7. Are the search options sensible?
      • The search options are sensible starting with a selection of cancer type, then heterogeneity and gene type. Additionally it provides an option to search based on mutation level based on its own compiled phylogenetic tree and specific gene event or gene | Intertumor Heterogeneity Page
    8. Run a sample query. Do the results make sense?
      • Looking at Intertumor Heterogeneity, I selected Cancer Type: Breast Cancer, Heterogeneity: Primary-Metastatic, and Gene Type: Cancer Gene Census. It provided 73 results that matched these certifications as well as a list of where the mutations occurred: The Trunk- mutation occurring in every tumor sub clone, The Branch- mutations present in tumor that are not present in every part of the tumor, and The Leaf- mutations mutations present in only one region. The results made sense and further provided a graph indicating what genes most commonly exhibited a mutation the allowing for further analysis on specific genes and mutations within the results. The results therefore make sense based on the basis of analyzing breast tumor mutations InterTumor Breast cancer Results
    9. Access: Is there a license agreement or any restrictions on access to the database?
      • There are no restrictions on access nor any license agreements on the page.

Summary judgment

    1. Would you direct a colleague unfamiliar with the field to use it?
      • The CancerTracer Database is extremely straightforward and therefore I would highly recommend it, if the topic pertains to the information available on the webpage.
    2. Is this a professional or "hobby" database? The "hobby" analogy means that it was that person's hobby to make the database. It could mean that it is limited in scope, done by one or a few persons, and/or seems amateur.
      • This page is not a "hobby" database based on the organization and density of information available on the page. The page is run by a Research and Development Laboratory in Cai University, China and therefore does not appear to be run by one or few amateur persons CancerTracer Contact Page
    3. Finally, please share why you chose this database in the first place, i.e., why did it interest you? Did it live up to the expectations you had when you chose it?
      • We chose this database because the purpose of the database strongly correlated to the purpose of the class and assignment; understanding how to successfully navigate and use pertinent information in academic and research articles. The subject of the database is tracing Cancer mutations which interested us because tumor heterogeneity is one of the largest issues faced by researchers and medical practitioners alike. The page did prove to be incredibly interesting and provided a vast amount of information in relation to the subect.

Scientific Conclusion

The outcome of this assignment was to navigate the CancerTracer database and analyze its components such as its data (compilation method, important, and content), user-friendliness, and database maintenance. The purpose of this assignment was to familiarize ourselves with databases and provide comfort with sorting through information and validity of the content and page.

Acknowledgements

  • We acknowledge [user:Taylor Makela] who we consulted on syntax and formatting of the webpage
  • Dr. Dahlquist
    • Dr. Dahlquist served as a coach for how to begin our pages. She also instructed the class and provided us with the guiding homework document.
  • We copied and modified the protocol shown on the Week 8 page of our class OpenWetWare.
  • Except for what is noted above, this individual journal entry was completed by us and not copied from another source


Nidapatel (talk) 21:03, 28 October 2020 (PDT) Jcorrey (talk) 21:25, 28 October 2020 (PDT)

References

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