Difference between revisions of "The Comprehensive Antibiotic Resistance Database"
From LMU BioDB 2017
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== Database Information == | == Database Information == | ||
* '''General information about the database''' | * '''General information about the database''' | ||
| − | *# | + | *# “CARD, the Comprehensive Antibiotic Resistance Database [https://card.mcmaster.ca/home]” |
| − | *# | + | *# “The Comprehensive Antibiotic Resistance Database ("CARD") provides data, models, and algorithms relating to the molecular basis of antimicrobial resistance.[https://card.mcmaster.ca/about]” |
| − | *## | + | *## It’s intended to be a general purpose database for all things antimicrobal, specifically including algorithms, models, sequences, and general information about them. [https://card.mcmaster.ca/about] |
| − | *## | + | *## 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. [https://card.mcmaster.ca/faq] |
| − | *##* | + | *##* Both types of sources are stored by CARD. [https://card.mcmaster.ca/faq] |
| − | *##* curated | + | *##* The data in CARD is from curated sources. [https://card.mcmaster.ca/faq] |
| − | *##* | + | *##* The data in CARD is curated by humans. [https://card.mcmaster.ca/faq] |
| − | *##* in | + | *##* The data in CARD is curated by professionals in the community. [https://card.mcmaster.ca/faq] |
| − | *# | + | *# “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. [https://card.mcmaster.ca/about]” |
| − | *#* public | + | *#* The CARD database is in the public domain. [https://card.mcmaster.ca/about] |
| − | *#* | + | *#* The CARD database was started by a small laboratory but is actively maintained by a global team of collaborators. [https://card.mcmaster.ca/about] |
| − | *# | + | *# “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). [https://card.mcmaster.ca/about]” |
* '''Scientific quality of the database''' | * '''Scientific quality of the database''' | ||
| − | *# | + | *# The content contains a detailed enough profile of antimicrobial resistance molecules to be useful to those studying the area given the community involvement. [https://card.mcmaster.ca/about] |
| − | *#* | + | *#* 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. [https://card.mcmaster.ca/download] |
| − | *#* | + | *#* 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. [https://www.ncbi.nlm.nih.gov/pubmed/27789705] |
| − | *# | + | *# Only species relating to antimicrobial resistance are categorized in CARD. [https://card.mcmaster.ca/about] |
| − | *# | + | *# 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. [https://card.mcmaster.ca/analyze] |
| − | *# | + | *# The data is updated on a monthly basis. [https://card.mcmaster.ca/about] |
| − | *#* | + | *#* 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. [https://twitter.com/arpcard] |
| − | *#* | + | *#* There are a few other databases operating in this specific field of research, like ARDB, MEGARes, and ARG-ANNOT [https://ardb.cbcb.umd.edu/], [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210519/], [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910750/] |
| − | *#* | + | *#* The paper describing their database is was released in July of 2013. [https://www.ncbi.nlm.nih.gov/pubmed/23650175] |
| − | *#* | + | *#* The database is updated monthly. [https://card.mcmaster.ca/about] |
| − | *#* | + | *#* The database was last updated on 2017-09-07 [https://card.mcmaster.ca/download] |
* '''General utility of the database to the scientific community''' | * '''General utility of the database to the scientific community''' | ||
*# Are there links to other databases? Which ones? | *# Are there links to other databases? Which ones? | ||
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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. [[User:Cazinge|Cazinge]] handled the first two sections, while [[User:Mbalducc|Mbalducc]] took care of the other two. | 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. [[User:Cazinge|Cazinge]] handled the first two sections, while [[User:Mbalducc|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. | While we worked together to complete this assignment, this database page was completed by us and not copied from another source. | ||
| + | |||
[[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 20:59, 2 October 2017 (PDT) | [[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 20:59, 2 October 2017 (PDT) | ||
Revision as of 04:19, 3 October 2017
Contents
Database Information
- General information about the database
- “CARD, the Comprehensive Antibiotic Resistance Database [1]”
- “The Comprehensive Antibiotic Resistance Database ("CARD") provides data, models, and algorithms relating to the molecular basis of antimicrobial resistance.[2]”
- It’s intended to be a general purpose database for all things antimicrobal, specifically including algorithms, models, sequences, and general information about them. [3]
- 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]
- “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]”
- “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
- 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]
- Only species relating to antimicrobial resistance are categorized in CARD. [16]
- 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]
- 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]
- The content contains a detailed enough profile of antimicrobial resistance molecules to be useful to those studying the area given the community involvement. [13]
- General utility of the database to the scientific community
- Are there links to other databases? Which ones?
- Is it convenient to browse the data?
- Is it convenient to download the data?
- In what file formats are the data provided?
- Are they standard or non-standard formats?
- Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
- 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?
- Access: Is there a license agreement or any restrictions on access to the database?
- Summary judgment
- Would you direct a colleague unfamiliar with the field to use it?
- Is this a professional or hobby database?
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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