Difference between revisions of "CRISPRlnc Group Journal"

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== Database Evaluation ==
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== CRISPRlnc Evaluation ==
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For your assignment, create a new wiki page to profile your database.  For this week, there will be one page per set of partners; both partners will contribute content and notes for their electronic lab notebook to the same page; you do not need to have separate individual journal entries for this week.
 
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* Use the name of the database as the name of your page. [[http://www.crisprlnc.org]]
 
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Read the article about the database from the ''Nucleic Acids Research'' journal and then go online to the database itself.  In keeping with Academic Honesty and citation practices, when you answer the questions below, provide a hyperlink to the page that you got the information from.  There should be at least one hyperlink per answer.
 
 
===General Information About the Database===
 
===General Information About the Database===
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# What is the name of the database? (link to the home page)
+
:1.''' What is the name of the database? (link to the home page)
−
#*We are utilizing the [http://www.crisprlnc.org CRISPRInc] Databse
+
::We are utilizing the [http://www.crisprlnc.org CRISPRInc] Databse
−
# What type (or types) of database is it?
+
:2.''' What type (or types) of database is it?
−
#*CRISPR is a database of  validated CRISPR/Cas9 sgRNAs "single guide RNA" for lncRNAs of model organisms "long non-coding RNA". From: Introduction to the 2019 ''NAR'' Database Issue: [https://academic.oup.com/nar/article/47/D1/D1/5280358 Rigden, D. J. & Fernández-Suárez, X. M. (2019). The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. Nucleic acids research, 47(D1): D1–D7. doi:10.1093/nar/gky1267] [https://academic.oup.com/nar/article/47/D1/D1/5280358]
+
::CRISPR is a database of  validated CRISPR/Cas9 sgRNAs "single guide RNA" for lncRNAs of model organisms "long non-coding RNA". From: Introduction to the 2019 ''NAR'' Database Issue: [https://academic.oup.com/nar/article/47/D1/D1/5280358 Rigden, D. J. & Fernández-Suárez, X. M. (2019). The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. Nucleic acids research, 47(D1): D1–D7. doi:10.1093/nar/gky1267] [https://academic.oup.com/nar/article/47/D1/D1/5280358]
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# What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
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:::'''a) What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
−
#*CRISPRlnc contains validated sgRNAs sequences and descriptions for model organisms lncRNAs.[http://www.crisprlnc.org]
+
::::CRISPRlnc contains validated sgRNAs sequences and descriptions for model organisms lncRNAs.[http://www.crisprlnc.org]
−
# What type of data source does it have?
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:::'''b) What type of data source does it have?
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#*CRISPlnc utilizes specific literature information from PubMed, NCBI and Ensemble.
+
::::CRISPlnc utilizes specific literature information from PubMed, NCBI and Ensemble. [https://academic.oup.com/nar/article/47/D1/D1/5280358]
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# Primary versus secondary ("meta")?
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:::::*'''Primary versus secondary ("meta")?
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#*CRISRlnc is a secondary source database. [http://www.crisprlnc.org]
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:::::::CRISRlnc is a secondary source database. [http://www.crisprlnc.org]
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# curated versus non-curated?
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:::::*'''Curated versus non-curated?
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#*This database is manually curated. [http://www.crisprlnc.org]
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:::::::This database is manually curated. [http://www.crisprlnc.org]
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# if curated, is it electronic versus human curation?
+
::::::::*'''If curated, is it electronic versus human curation?
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#*Human curation [http://www.crisprlnc.org/]
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::::::::::Human curation [http://www.crisprlnc.org/]
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# if human curation, is it in-house staff versus community curation?
+
:::::::::::*'''If human curation, is it in-house staff versus community curation?
−
#*In-house curation. [http://www.crisprlnc.org/]
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:::::::::::::In-house curation. [http://www.crisprlnc.org/]
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# What individual or organization maintains the database?
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:3.''' What individual or organization maintains the database?
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#*CRISPRlnc is maintained by Bioinformatics Group of XTBG [http://www.crisprlnc.org/]
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::CRISPRlnc is maintained by Bioinformatics Group of XTBG [http://www.crisprlnc.org/]
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# public versus private
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:*''' Public versus private
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#*this database is public [http://www.crisprlnc.org]
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::::This database is public [http://www.crisprlnc.org]
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# large national or multinational entity or small lab group
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:*'''Large national or multinational entity or small lab group
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#*CRISPR is based in the Bioinformatics group of the Xishuangbanna Tropical Botanical Garden, of the Chinese Academy of Sciences. However, the tool created through this lab has gained international renown. [http://www.crisprlnc.org]
+
::::CRISPR is based in the Bioinformatics group of the Xishuangbanna Tropical Botanical Garden, of the Chinese Academy of Sciences. However, the tool created through this lab has gained international renown. [http://www.crisprlnc.org]
−
# What is their funding source(s)?  
+
:4.''' What is their funding source(s)?  
−
#*CRISPR is funded by The National Natural Science Foundation of China, Yunnan Province, The Scientific Research Fund of Hunan Provincial Education Department and The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province[https://academic.oup.com/nar/article/47/D1/D1/5280358]
+
::CRISPR is funded by The National Natural Science Foundation of China, Yunnan Province, The Scientific Research Fund of Hunan Provincial Education Department and The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province[https://academic.oup.com/nar/article/47/D1/D1/5280358]
  
 
===Scientific Quality of the Database===
 
===Scientific Quality of the Database===
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# Does the content appear to completely cover its content domain?
+
:1.''' Does the content appear to completely cover its content domain?
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#* How many records does the database contain?
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::All content is included through an outline stating what exactly is in the database.
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#** The database contains  2089 records of collected sgRNA data.  
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:::*''' How many records does the database contain?
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#* What claims do the database owners make about coverage in the corresponding paper?   
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::::: The database contains  2089 records of collected sgRNA data.  
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#** 7
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:::*''' What claims do the database owners make about coverage in the corresponding paper?   
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# What species are covered in the database? (If it is a ''very'' long list, summarize.)
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::::: None
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#* This database covers:''Homo sapiens''(Humans), ''Mus musculus'' (Mouse),  ''Drosophila melanogaster'' (Fly), ''Rattus norvegicus'' (Brown Rat), ''Oryctolagus cuniculus'' (European Rabbit), ''Sus scrofa'' (Wild Boar), ''danio rerio'' (Zebrafish), and ''solanum lycopersicum'' (Tomatoes)
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:2.''' What species are covered in the database? (If it is a ''very'' long list, summarize.)
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# Is the database content useful? I.e., what biological questions can it be used to answer?
+
:: This database covers:''Homo sapiens''(Humans), ''Mus musculus'' (Mouse),  ''Drosophila melanogaster'' (Fly), ''Rattus norvegicus'' (Brown Rat), ''Oryctolagus cuniculus'' (European Rabbit), ''Sus scrofa'' (Wild Boar), ''danio rerio'' (Zebrafish), and ''solanum lycopersicum'' (Tomatoes)
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# Is the database content timely?
+
:3.''' Is the database content useful? I.e., what biological questions can it be used to answer?
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# Is there a need in the scientific community for such a database at this time?
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::::: Yes it is, this database provides all necessary information about lncRNA in a verified and professional manner in order to help greater understand lncRNA and their individual benefits/functions.
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#* Is the content covered by other databases already?
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:4.''' Is the database content timely?
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# How ''current'' is the database?
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:::*''' Is there a need in the scientific community for such a database at this time?
−
#* When did the database first go online?
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::::: Yes, lncRNA is relatively undiscovered in terms of information, and so this database can help speed the process of information collection/reference to create a standard for how this type of biological data should be presented.
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#** May 18th, 2018
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:::*''' Is the content covered by other databases already?
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# How often is the database updated?
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::::: Only a select few databases cover this conent.
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#* When was the last update?
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:5.''' How ''current'' is the database?
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#** February 12th, 2019
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:::*''' When did the database first go online?
 +
::::: May 18th, 2018
 +
:::*''' When was the last update?
 +
::::: February 12th, 2019
  
 
===General Utility of the Database to the Scientific Community===
 
===General Utility of the Database to the Scientific Community===
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*# Are there links to other databases?  Which ones?
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:1.''' Are there links to other databases?  Which ones?
−
*# Is it convenient to browse the data?
+
::::: Yes: NONCode,lncrnadb, CRlncRNA, Lnc2Cancer, LncSNP 2,0, and CRISPRz
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*# Is it convenient to download the data?
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:2.''' Is it convenient to browse the data?
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*#* In what file formats are the data provided?
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::::: Yes
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*#** What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
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:3.''' Is it convenient to download the data?
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*#** Are they standard or non-standard formats?  (i.e., are they following an approved standard for that type of data)?
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::::: Yes
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*# Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?   
+
::*''' In what file formats are the data provided?
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*#* Is the website well-organized?   
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::::: .xlsx, .fa, and .bed
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*#* Does it have a help section or tutorial?   
+
::::*''' What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
−
*#* Are the search options sensible?
+
::::: The files are available in .xslx, .fa, and .bed files, however, each file differs based on the data presented.
−
*#* Run a sample query.  Do the results make sense?
+
::::*''' Are they standard or non-standard formats?  (i.e., are they following an approved standard for that type of data)?
−
*# Access:  Is there a license agreement or any restrictions on access to the database?
+
::::: The file types are generally not used in order to display this typer of data, certain users may have to download applications in order to open these file types.
 +
:4.''' Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?   
 +
::*''' Is the website well-organized?   
 +
::::: Yes, it is very well organized and placement of information makes sense.
 +
::*''' Does it have a help section or tutorial?   
 +
::::: Yes, however the help/documentation section is somewhat small.
 +
::*''' Are the search options sensible?
 +
::::: Yes
 +
::*''' Run a sample query.  Do the results make sense?
 +
::::: Yes
 +
:5.''' Access:  Is there a license agreement or any restrictions on access to the database?
 +
::::: No, the database is unrestricted
  
 
===Summary Judgment===
 
===Summary Judgment===
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*# Would you direct a colleague unfamiliar with the field to use it?
+
:1.''' Would you direct a colleague unfamiliar with the field to use it?
−
*# 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.
+
:::: Yes, CRISPRlnc is very easily accessible, simple to navigate, and provides very insightful, verified, information.
 +
:2.''' Is this a professional or "hobby" database?
 +
::::This database is a professional one.
 +
 
 +
===Presentation===
 +
[[File:CRISPR_PResentation12.pptx ]]
  
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==== Some Definitions ====
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===Acknowledgements===
  
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* Electronic curation occurs when someone writes a program to add information to a database record from another database.
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* We would like to thank [[User:Kdahlquist| Dr. Kam Dahlquist]] for the introduction to the databases utilized during this research assignment.
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* Manual curation occurs when a human reviews the information being added to a record to validate it as true.
+
* Thank you to my homework partner [[User:dramir36| David Ramirez]] for his partnership in this assignment. We met in person and spoke over the phone in order to discuss the sharing of responsibility, contents of the page, presentation ordering and formatting
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** In-house is when the human works for the database organization.
+
*Except for what is noted above, this journal entry was done by me and not copied from another source. [[User:Jnimmers|Jnimmers]] ([[User talk:Jnimmers|talk]]) 23:59, 30 September 2019 (PDT)
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** Community is when the database allows members of the scientific community that don't work for the database organization to add information to the record.
+
*Worked with [[User:Jnimmers| John Nimmers-Minor]] inside and outside of class to complete this project and powerpoint.
 +
*Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
 +
[[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 00:05, 1 October 2019 (PDT)
 +
[[Journal Entry]]

Latest revision as of 13:19, 1 October 2019

CRISPRlnc Evaluation

General Information About the Database

1. What is the name of the database? (link to the home page)
We are utilizing the CRISPRInc Databse
2. What type (or types) of database is it?
CRISPR is a database of validated CRISPR/Cas9 sgRNAs "single guide RNA" for lncRNAs of model organisms "long non-coding RNA". From: Introduction to the 2019 NAR Database Issue: Rigden, D. J. & Fernández-Suárez, X. M. (2019). The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. Nucleic acids research, 47(D1): D1–D7. doi:10.1093/nar/gky1267 [1]
a) What biological information (type of data) does it contain? (sequence, structure, model organism, or specialty [what?])
CRISPRlnc contains validated sgRNAs sequences and descriptions for model organisms lncRNAs.[2]
b) What type of data source does it have?
CRISPlnc utilizes specific literature information from PubMed, NCBI and Ensemble. [3]
  • Primary versus secondary ("meta")?
CRISRlnc is a secondary source database. [4]
  • Curated versus non-curated?
This database is manually curated. [5]
  • If curated, is it electronic versus human curation?
Human curation [6]
  • If human curation, is it in-house staff versus community curation?
In-house curation. [7]
3. What individual or organization maintains the database?
CRISPRlnc is maintained by Bioinformatics Group of XTBG [8]
  • Public versus private
This database is public [9]
  • Large national or multinational entity or small lab group
CRISPR is based in the Bioinformatics group of the Xishuangbanna Tropical Botanical Garden, of the Chinese Academy of Sciences. However, the tool created through this lab has gained international renown. [10]
4. What is their funding source(s)?
CRISPR is funded by The National Natural Science Foundation of China, Yunnan Province, The Scientific Research Fund of Hunan Provincial Education Department and The Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province[11]

Scientific Quality of the Database

1. Does the content appear to completely cover its content domain?
All content is included through an outline stating what exactly is in the database.
  • How many records does the database contain?
The database contains 2089 records of collected sgRNA data.
  • What claims do the database owners make about coverage in the corresponding paper?
None
2. What species are covered in the database? (If it is a very long list, summarize.)
This database covers:Homo sapiens(Humans), Mus musculus (Mouse), Drosophila melanogaster (Fly), Rattus norvegicus (Brown Rat), Oryctolagus cuniculus (European Rabbit), Sus scrofa (Wild Boar), danio rerio (Zebrafish), and solanum lycopersicum (Tomatoes)
3. Is the database content useful? I.e., what biological questions can it be used to answer?
Yes it is, this database provides all necessary information about lncRNA in a verified and professional manner in order to help greater understand lncRNA and their individual benefits/functions.
4. Is the database content timely?
  • Is there a need in the scientific community for such a database at this time?
Yes, lncRNA is relatively undiscovered in terms of information, and so this database can help speed the process of information collection/reference to create a standard for how this type of biological data should be presented.
  • Is the content covered by other databases already?
Only a select few databases cover this conent.
5. How current is the database?
  • When did the database first go online?
May 18th, 2018
  • When was the last update?
February 12th, 2019

General Utility of the Database to the Scientific Community

1. Are there links to other databases? Which ones?
Yes: NONCode,lncrnadb, CRlncRNA, Lnc2Cancer, LncSNP 2,0, and CRISPRz
2. Is it convenient to browse the data?
Yes
3. Is it convenient to download the data?
Yes
  • In what file formats are the data provided?
.xlsx, .fa, and .bed
  • What type of files, indicated by the file extension (e.g., .txt, .xml., etc.)?
The files are available in .xslx, .fa, and .bed files, however, each file differs based on the data presented.
  • Are they standard or non-standard formats? (i.e., are they following an approved standard for that type of data)?
The file types are generally not used in order to display this typer of data, certain users may have to download applications in order to open these file types.
4. Evaluate the “user-friendliness” of the database: can a naive user quickly navigate the website and gather useful information?
  • Is the website well-organized?
Yes, it is very well organized and placement of information makes sense.
  • Does it have a help section or tutorial?
Yes, however the help/documentation section is somewhat small.
  • Are the search options sensible?
Yes
  • Run a sample query. Do the results make sense?
Yes
5. Access: Is there a license agreement or any restrictions on access to the database?
No, the database is unrestricted

Summary Judgment

1. Would you direct a colleague unfamiliar with the field to use it?
Yes, CRISPRlnc is very easily accessible, simple to navigate, and provides very insightful, verified, information.
2. Is this a professional or "hobby" database?
This database is a professional one.

Presentation

File:CRISPR PResentation12.pptx

Acknowledgements

  • We would like to thank Dr. Kam Dahlquist for the introduction to the databases utilized during this research assignment.
  • Thank you to my homework partner David Ramirez for his partnership in this assignment. We met in person and spoke over the phone in order to discuss the sharing of responsibility, contents of the page, presentation ordering and formatting
  • Except for what is noted above, this journal entry was done by me and not copied from another source. Jnimmers (talk) 23:59, 30 September 2019 (PDT)
  • Worked with John Nimmers-Minor inside and outside of class to complete this project and powerpoint.
  • Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Dramir36 (talk) 00:05, 1 October 2019 (PDT) 

Journal Entry
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