The Comprehensive Antibiotic Resistance Database - Revision history

Cazinge: Fixing link

2017-10-03T17:40:24Z

Fixing link

Cazinge: adding database link

2017-10-03T07:00:55Z

adding database link

Mbalducc: /* References */

2017-10-03T04:48:37Z

‎References

Mbalducc: /* Mbalducc's Response */

2017-10-03T04:47:23Z

‎Mbalducc's Response

Cazinge: /* Electronic Notebook */ Adding notebook summaries

2017-10-03T04:45:38Z

‎Electronic Notebook: Adding notebook summaries

Cazinge: /* Database Information */ fixing formatting

2017-10-03T04:30:49Z

‎Database Information: fixing formatting

Cazinge: Added Structure

2017-10-03T04:28:25Z

Added Structure

Cazinge: Uploading Mbalducc's responses

2017-10-03T04:27:01Z

Uploading Mbalducc's responses

Cazinge: Uploading Cazinge's Section

2017-10-03T04:19:10Z

Uploading Cazinge's Section

Mbalducc: added my signature

2017-10-03T04:05:54Z

added my signature

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 == Database Link ==
-https://docs.google.com/presentation/d/14AX-1gyfzkLq5AeHAmgLn0JkaPwetYxKA97IDxn-Rrk/edit?usp=sharing
+{{Media:The Comprehensive Antibiotic Database.pdf}}
 === Acknowledgements ===

@@ Line 59: / Line 59: @@
 * 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.
 === Acknowledgements ===

@@ Line 70: / Line 70: @@
 === References ===
-LMU BioDB 2017. (2017). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_1
+Journals.ASM.org (2017). The Comprehensive Antibiotic Resistance Database. Retrieved October 1, 2017, from http://aac.asm.org/content/57/7/3348.full.pdf
 == Other Links ==

@@ Line 58: / Line 58: @@
 * 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, and took some screenshots of the website to give it visuals and hopefully make it easier to understand.
+* 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.
 === Acknowledgements ===

← Older revision		Revision as of 04:45, 3 October 2017
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	=== Electronic Notebook ===		=== 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, and took some screenshots of the website to give it visuals and hopefully make it easier to understand.

	=== Acknowledgements ===		=== Acknowledgements ===

@@ Line 28: / Line 28: @@
 *# Yes, there are links to the NCBI taxonomy and NCBI Gene databases. [https://card.mcmaster.ca/faq]
 *# 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. [https://card.mcmaster.ca/ontology/36006]
+*#* 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. [https://card.mcmaster.ca/ontology/36006]
-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. [https://card.mcmaster.ca/ontology/40323]
+*#* 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. [https://card.mcmaster.ca/ontology/40323]
 *# 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:
+*#* Data is in at least one of these file formats:  JSON, TAB, OBO, FASTA, OWL, XML, CSV, PYTHON, TXT, GZ [https://card.mcmaster.ca/download]
 *#* All the file formats are standard.  [https://en.wikipedia.org/wiki/List_of_file_formats]
 *# Website is not super user-friendly. I felt confused using it, especially without computer science knowledge. [https://card.mcmaster.ca]

@@ Line 43: / Line 43: @@
 *# 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. [https://card.mcmaster.ca/home]
 *# 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. [https://card.mcmaster.ca/home]
 === Acknowledgements ===
@@ Line 56: / Line 58: @@
 LMU BioDB 2017. (2017). Week 1. Retrieved August 29, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_1
 {{Template:Cazinge}}
 {{Template:Mbalducc}}

@@ Line 26: / Line 26: @@
 *#* The database was last updated on 2017-09-07 [https://card.mcmaster.ca/download]
 * '''General utility of the database to the scientific community'''
-*# Are there links to other databases?  Which ones?
+*# Yes, there are links to the NCBI taxonomy and NCBI Gene databases. [https://card.mcmaster.ca/faq]
-*# Is it convenient to browse the data?
+*# Browsing the data is convenient, there are two sections to browse under:
-*# Is it convenient to download the data?
+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. [https://card.mcmaster.ca/ontology/36006]
-*#* In what file formats are the data provided?
+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. [https://card.mcmaster.ca/ontology/40323]
-*#* Are they standard or non-standard formats?
+*# Downloading the data is convenient. It's organized into categories: CARD Data, CARD Data changes, CARD Prevalence Data, Software
-*# Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
+Data is in at least one of these file formats:
-*#* Is the website well-organized?
+*#* JSON, TAB, OBO, FASTA, OWL, XML, CSV, PYTHON, TXT, GZ [https://card.mcmaster.ca/download]
-*#* Does it have a help section or tutorial?
+*#* All the file formats are standard.  [https://en.wikipedia.org/wiki/List_of_file_formats]
-*#* Are the search options sensible?
+*# Website is not super user-friendly. I felt confused using it, especially without computer science knowledge. [https://card.mcmaster.ca]
-*#* Run a sample query.  Do the results make sense?
+*#* Well organized, everything is within categories that become more and more specific [https://card.mcmaster.ca]
-*# Access:  Is there a license agreement or any restrictions on access to the database?
+*#* There is no tutorial or help section. But, there is contact info for the makers and there is an FAQ section. [https://card.mcmaster.ca/faq]
 * '''Summary judgment'''
-*# Would you direct a colleague unfamiliar with the field to use it?
+*# 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. [https://card.mcmaster.ca/home]
-*# Is this a professional or hobby database?
+*# 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. [https://card.mcmaster.ca/home]
 === Acknowledgements ===

@@ Line 1: / Line 1: @@
 == Database Information ==
 * '''General information about the database'''
-*# What is the name of the database? (link to the home page)
+*# “CARD, the Comprehensive Antibiotic Resistance Database [https://card.mcmaster.ca/home]”
-*# What type (or types) of database is it?
+*# “The Comprehensive Antibiotic Resistance Database ("CARD") provides data, models, and algorithms relating to the molecular basis of antimicrobial resistance.[https://card.mcmaster.ca/about]”
-*## What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
+*## 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]
-*## What type of data source does it have?
+*## 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]
-*##* primary versus secondary ("meta")
+*##* Both types of sources are stored by CARD. [https://card.mcmaster.ca/faq]
-*##* curated versus non-curated
+*##* The data in CARD is from curated sources. [https://card.mcmaster.ca/faq]
-*##* electronic versus human curation
+*##* The data in CARD is curated by humans. [https://card.mcmaster.ca/faq]
-*##* in-house staff versus community curation
+*##* The data in CARD is curated by professionals in the community.  [https://card.mcmaster.ca/faq]
-*# What individual or organization maintains the database?
+*# “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 versus private
+*#* The CARD database is in the public domain. [https://card.mcmaster.ca/about]
-*#* large national or multinational entity or small lab group
+*#* The CARD database was started by a small laboratory but is actively maintained by a global team of collaborators. [https://card.mcmaster.ca/about]
-*# What is their funding source(s)?
+*# “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'''
-*# Does the content appear to completely cover its content domain?
+*# 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]
-*#* How many records does the database contain?
+*#* 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]
-*#* What claims do the database owners make about coverage in the corresponding paper?
+*#* 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]
-*# What species are covered in the database?
+*# Only species relating to antimicrobial resistance are categorized in CARD. [https://card.mcmaster.ca/about]
-*# Is the database content useful? I.e., what biological questions can it be used to answer?
+*# 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]
-*# Is the database content timely?
+*# The data is updated on a monthly basis. [https://card.mcmaster.ca/about]
-*#* Is there a need in the scientific community for such a database at this time?
+*#* 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]
-*#* Is the content covered by other databases already?
+*#* 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/]
-*#* When did the database first go online?
+*#* The paper describing their database is was released in July of 2013. [https://www.ncbi.nlm.nih.gov/pubmed/23650175]
-*#* How often is the database updated?
+*#* The database is updated monthly. [https://card.mcmaster.ca/about]
-*#* When was the last update?
+*#* The database was last updated on 2017-09-07 [https://card.mcmaster.ca/download]
 * '''General utility of the database to the scientific community'''
 *# Are there links to other databases?  Which ones?
@@ Line 45: / Line 45: @@
 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.
 [[User:Cazinge|Cazinge]] ([[User talk:Cazinge|talk]]) 20:59, 2 October 2017 (PDT)

← Older revision		Revision as of 04:05, 3 October 2017
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	[[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)

		+	[[User:Mbalducc\|Mbalducc]] ([[User talk:Mbalducc\|talk]]) 21:05, 2 October 2017 (PDT)

	=== References ===		=== References ===