Revision as of 04:30, 3 October 2017

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

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

LMU BioDB 2017. (2017). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_1

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