Database Information

General information about the database
1. “CARD, the Comprehensive Antibiotic Resistance Database [1]”
2. “The Comprehensive Antibiotic Resistance Database ("CARD") provides data, models, and algorithms relating to the molecular basis of antimicrobial resistance.[2]”
  1. It’s intended to be a general purpose database for all things antimicrobal, specifically including algorithms, models, sequences, and general information about them. [3]
  2. The CARD is curated by a group of experts in the area of antimicrobial resistance (AMR) and bioinformatics, including consultation with outside experts where needed. [4]
    - Both types of sources are stored by CARD. [5]
    - The data in CARD is from curated sources. [6]
    - The data in CARD is curated by humans. [7]
    - The data in CARD is curated by professionals in the community. [8]
3. “The CARD was designed and developed by the laboratories of Drs. Gerry Wright and Andrew G. McArthur of McMaster University's Department of Biochemistry & Biomedical Sciences (Hamilton, Ontario, Canada) with the help of a global team of collaborators. [9]”
  - The CARD database is in the public domain. [10]
  - The CARD database was started by a small laboratory but is actively maintained by a global team of collaborators. [11]
4. “Their research has been supported by funds from the Canadian Foundation for Innovation, Canadian Institutes of Health Research, Natural Sciences and Engineering Research Council of Canada, Medical Research Council (UK), and Ontario Research Fund, as well as a Cisco Research Chair in Bioinformatics supported by Cisco Systems Canada, Inc. (Dr. McArthur), Canada Research Chair (Dr. Wright), and Killam Research Fellowship (Dr. Wright). [12]”
Scientific quality of the database
1. The content contains a detailed enough profile of antimicrobial resistance molecules to be useful to those studying the area given the community involvement. [13]
  - While the database contains a limited amount of information, currently around 3000 entries (13 MB worth of data) in json and various other file formats, the main use of CARD is provided through the easy to use tools for analysis that they include on their website. [14]
  - They claim that the information in CARD allows for meaningful analysis via their tools, and is comprehensive enough for admittedly “novel” analysis tools to be created due to their repository of information. [15]
2. Only species relating to antimicrobial resistance are categorized in CARD. [16]
3. The data can be used to perform a multitude of analytics on the various species included in the database, especially using their tools for performing BLAST searches and visualizing RGI information. [17]
4. The data is updated on a monthly basis. [18]
  - Given the somewhat high amount of presence, (343 followers) of their social media platform, I can only imagine that their data is useful to the subset of Biologists studying their specific area of research. [19]
  - There are a few other databases operating in this specific field of research, like ARDB, MEGARes, and ARG-ANNOT [20], [21], [22]
  - The paper describing their database is was released in July of 2013. [23]
  - The database is updated monthly. [24]
  - The database was last updated on 2017-09-07 [25]
General utility of the database to the scientific community
1. Yes, there are links to the NCBI taxonomy and NCBI Gene databases. [26]
2. Browsing the data is convenient, there are two sections to browse under:
  - ARO: The Antibiotic Resistance Ontology → organizes data on antibiotic resistance and antibiotics. Clicking on this link takes you to a page with the definition of “antibiotic resistance” and links to pages for more terms that come under that category (for example: antibiotic molecule, antibiotic biosynthesis, etc…). Each of those contain links to more specific pages, and so on. This allows you to start with a general idea, and find more and more specific information as you navigate deeper into the database. [27]
  - Model Ontology: Organizes determinants for antibiotic resistance. They are organized by models which refer to how the resistance comes about. For example, there are sequences which will always cause resistance, the “protein homolog” model, and sequences which determine resistance through mutations and variations, the “protein variant” model. There are other models as well. Like in the ARO section, the data is organized into groups and sub groups which become more and more specific. [28]
3. Downloading the data is convenient. It's organized into categories: CARD Data, CARD Data changes, CARD Prevalence Data, Software
  - Data is in at least one of these file formats: JSON, TAB, OBO, FASTA, OWL, XML, CSV, PYTHON, TXT, GZ [29]
  - All the file formats are standard. [30]
4. Website is not super user-friendly. I felt confused using it, especially without computer science knowledge. [31]
  - Well organized, everything is within categories that become more and more specific [32]
  - There is no tutorial or help section. But, there is contact info for the makers and there is an FAQ section. [33]
  - There is a search bar, but no search options. All possible search results including synonyms and related terms are shown. The browse section requires that you follow a pathway to something specific by clicking links within pages. [34]
  - I did a test search for penicillin, the results made sense. I got results for penicillin and derivatives, as well as penicillin resistance sequences, and other terms related to penicillin. [35]
5. The database does not require any license or membership to use. It is free and accessible to the public and the tools and data are available for non-commercial, research and academic use. To use commercially, permission is required as well as a user fee. [36]
Summary judgment
1. I probably wouldn’t suggest that someone unfamiliar with this field use this database. It’s written in very technical terms and the search is not easy to use unless you know exactly what you are looking for. [37]
2. This seems more like a professional database, it is set up in a way that is not necessarily intuitive for someone not experienced in this field. [38]

Electronic Notebook

Cazinge's Response

When we first chose this database, it looked great, the UI looked reasonably friendly, the color scheme was inviting, and the topic of the database seemed interesting enough to warrant attention from users that weren't necessarily affiliated with the field. As we attempted to navigate the website for information, however, it was difficult to find exactly what we were looking for, given that the meta information surrounding the database wasn't very comprehensive.
Even after inspecting the site, I still don't feel as if I have a very comprehensive understanding of what The Antimicrobial Resistance part of the database's name actually means. As such, answering these questions took quite a bit of time and effort, in order to decipher what was important from what was irrelevant for my needs.
In order to effectively do so, I first attempted to collate all of the data that I was able to find on my own through the site. Then, I downloaded the data and made inferences as to how I thought the database worked as well as the more technical aspects of what it's focus was. Finally, I went online, found similar databases, and revisited the page with this information, now able to understand most of the information that I couldn't decipher on my own. That ordeal made me realize that this is a database moreso focused towards professional users who work with the data daily.
After that, Mbalducc and I created a presentation that adhered to the guidelines that professor Dahlquist laid out in class.

Mbalducc's Response

I started by visiting the database and just clicking around to get an idea for it was set up and the type of information it held.
Next, I began answering my set of questions by clicking through the database and performing searches, as well as checking out the Downloads, FAQ, and About sections.
I also found a article online about the creation of the CARD so I read through that to find information on the terminology the database uses, the type of data it holds, and why it was created.
I took notes on this information to put onto the wiki page.
I also used the information to make the presentation with Eddie, and took some screenshots of the website to give it visuals and hopefully make it easier to understand.

Database Link

Media:The Comprehensive Antibiotic Database.pdf

Acknowledgements

The two of us met outside of class on two separate occasions, and worked on two separate parts of the information gathering part of the assignment individually. Cazinge handled the first two sections, while Mbalducc took care of the other two. While we worked together to complete this assignment, this database page was completed by us and not copied from another source.

Cazinge (talk) 20:59, 2 October 2017 (PDT)

Mbalducc (talk) 21:05, 2 October 2017 (PDT)

References

Comprehensive Antibiotic Resistance Database. (2017). Retrieved September 29, 2017, from https://card.mcmaster.ca/

Journals.ASM.org (2017). The Comprehensive Antibiotic Resistance Database. Retrieved October 1, 2017, from http://aac.asm.org/content/57/7/3348.full.pdf

LMU BioDB 2017. (2017). Week 5. Retrieved September 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_5