CancerSEA Week 5

General Info

1. What is the name of the database?
   

   CancerSEA Homepage
   • CancerSEA
2. What type (or types) of database is it?
   • CancerSEA is a database that decodes the various functions of cancer cells.
   • What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])

     -It includes the breakdown of different cancer cells that have a specific functions (ie. apoptosis, DNA damage, proliferation)

     -It provides the location of where these cells are usually found in its active form

     -It states the genes that are involved with each cell's functionality

   • What type of data source does it have? (primary versus secondary ("meta")? curated versus non-curated? if curated, is it electronic versus human curation? if human curation, is it in-house staff versus community curation?)

     -CancerSEA obtains its data through secondary sources

     -It is curated data extracted by electronic curation

3. What individual or organization maintains the database? (public versus private? large national or multinational entity or small lab group?)
   • The organization that maintains the database is the College of Bioinformatics Science and Technology, an pubic and international university in China.
4. What is their funding source(s)?
   • CancerSEA obtains funding through the college and Harbin University of Medicine.

Science Quality

1. Does the content appear to completely cover its content domain?
   • How many records does the database contain?

   -The database contains about 42,000 records of single cancer cell sets.

   • What claims do the database owners make about coverage in the corresponding paper?

   -The owners claim on the paper that this database will be critical to cancer research as the sequencing of the function of cancer at the single cell is new and needed.

   -The ability to determine the heterogeneity of these cancers can be crucial to preventing excessive growth and spread of the cancers.

2. What species are covered in the database? (If it is a very long list, summarize.)

   -The species that are covered within the database include carcinomas, melanomas, leukemias, or cancers that are present in different body parts, ie. cervix cancer or renal cell cancer.

3. Is the database content useful? I.e., what biological questions can it be used to answer?

   -Yes. Since there is no single cure-all for all cancer cells, this data is useful for determining what kind of genes could be the target of potential medical treatments.

4. Is the database content timely?

   -The database content is timely because cancer research is always needed and always useful.

   • Is there a need in the scientific community for such a database at this time?

   -Yes, there is a need in the scientific community for this database at this time because not only can it be used in the educational or research setting, but it could be used for used for the creation of medical treatments. For example, medical physicians or oncologists could use it to aid in diagnoses based on what the cancer cells seem to be doing.

   • Is the content covered by other databases already?

   -No, this in-depth content does not seem to be covered by other databases.

5. How current is the database?
   • When did the database first go online?

   -The database first went online in 2018.

   • How often is the database updated? When was the last update?

   -There is currently no information as to how often the database was update, nor is there any information as to when the last update was.

General Utility

1. Are there links to other databases? Which ones?
   • This database links to Ensembl
2. Is it convenient to browse the data?
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)?
4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?

   -It might be a little difficult for someone who does not understand the content to navigate the site. There are many acronyms as well as terminologies that for the most part someone who was researching cancer cells would know.

   • Is the website well-organized?
   • Does it have a help section or tutorial?
   • Are the search options sensible?
   • Run a sample query. Do the results make sense?
5. Access: Is there a license agreement or any restrictions on access to the database?

Summary Judgement

1. Would you direct a colleague unfamiliar with the field to use it?
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 seems amateur.