IDog Week 5 - Revision history

Marmas: /* Acknowledgements */ added line breaks between signatures

2019-10-03T04:50:56Z

‎Acknowledgements: added line breaks between signatures

Marmas: /* Acknowledgements */ bolded statement and added signature

2019-10-03T04:50:33Z

‎Acknowledgements: bolded statement and added signature

Marmas: /* References */ removed annotation for reference

2019-10-03T04:49:57Z

‎References: removed annotation for reference

Jcowan4: fixed out line

2019-10-03T04:09:50Z

fixed out line

Jcowan4: /* Downloads */ made a header instead of subtopic

2019-10-03T04:09:13Z

‎Downloads: made a header instead of subtopic

Jcowan4: added presentation

2019-10-03T03:55:18Z

added presentation

Jcowan4: references

2019-10-03T03:45:21Z

references

Jcowan4: /* Summary */ added more data and fixed typos

2019-10-03T03:19:18Z

‎Summary: added more data and fixed typos

Jcowan4: /* General utility of the database to the scientific community */ design fix

2019-10-03T02:55:09Z

‎General utility of the database to the scientific community: design fix

Jcowan4: /* General utility of the database to the scientific community */ grammar and added more sentances

2019-10-03T02:54:29Z

‎General utility of the database to the scientific community: grammar and added more sentances

@@ Line 32: / Line 32: @@
 '''Except for what is noted above, this individual journal entry was completed by me and not copied from another source.'''
-[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 18:25, 2 October 2019 (PDT)
+[[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 18:25, 2 October 2019 (PDT)<br>
 [[User:Marmas|Marmas]] ([[User talk:Marmas|talk]]) 21:50, 2 October 2019 (PDT)

@@ Line 30: / Line 30: @@
 *I, Jonar Cowan, would like to acknowledge my homework partner, Michael Armas, for helping with the gathering of information, the creation of this page, and meeting up to go over presentation skills/ what to expect.
 *Dr. Dahlquist for the continued support in assisting and answering our questions during the making of this assignment.
-*Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
+'''Except for what is noted above, this individual journal entry was completed by me and not copied from another source.'''
 [[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 18:25, 2 October 2019 (PDT)
 ==References==

@@ Line 36: / Line 36: @@
 ==References==
-Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., ... & Zhang, Y. P. (2018). iDog: an integrated resource for domestic dogs and wild canids. Nucleic acids research, 47(D1), D793-D800. Accessed. September 26th (article for database)
+Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., ... & Zhang, Y. P. (2018). iDog: an integrated resource for domestic dogs and wild canids. Nucleic acids research, 47(D1), D793-D800. Accessed. September 26th
 LMU BioDB 2019. (2019). Week 5. Retrieved October 1, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5

@@ Line 26: / Line 26: @@
 This database was not made by an amateur. As it is a published database through a credible source, this database should not be classified as a "hobby" database. The database should be counted as professional, due to all the information and is possibly easily navigatable for experts in the field.
-===Acknowledgements===
+==Acknowledgements==
 *I, Michael Armas, would like to acknowledge my homework partner, Jonar Cowan, for helping with the gathering of information as well as for the creation of this page.
 *I, Jonar Cowan, would like to acknowledge my homework partner, Michael Armas, for helping with the gathering of information, the creation of this page, and meeting up to go over presentation skills/ what to expect.
@@ Line 34: / Line 34: @@
 [[User:Jcowan4|Jcowan4]] ([[User talk:Jcowan4|talk]]) 18:25, 2 October 2019 (PDT)
-===References===
+==References==
 Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., ... & Zhang, Y. P. (2018). iDog: an integrated resource for domestic dogs and wild canids. Nucleic acids research, 47(D1), D793-D800. Accessed. September 26th (article for database)

@@ Line 40: / Line 40: @@
 LMU BioDB 2019. (2019). Week 5. Retrieved October 1, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5
-===Downloads===
+==Downloads==
 Presentation: [[File:IDog_Presentation.pdf | iDog Slides]]

← Older revision		Revision as of 03:55, 3 October 2019
Line 40:		Line 40:
	LMU BioDB 2019. (2019). Week 5. Retrieved October 1, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5		LMU BioDB 2019. (2019). Week 5. Retrieved October 1, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5

		+	===Downloads===
		+	Presentation: [[File:IDog_Presentation.pdf \| iDog Slides]]

	==Misc.==		==Misc.==

← Older revision		Revision as of 03:45, 3 October 2019
Line 33:		Line 33:

	[[User:Jcowan4\|Jcowan4]] ([[User talk:Jcowan4\|talk]]) 18:25, 2 October 2019 (PDT)		[[User:Jcowan4\|Jcowan4]] ([[User talk:Jcowan4\|talk]]) 18:25, 2 October 2019 (PDT)
		+
		+	===References===
		+
		+	Tang, B., Zhou, Q., Dong, L., Li, W., Zhang, X., Lan, L., ... & Zhang, Y. P. (2018). iDog: an integrated resource for domestic dogs and wild canids. Nucleic acids research, 47(D1), D793-D800. Accessed. September 26th (article for database)
		+
		+	LMU BioDB 2019. (2019). Week 5. Retrieved October 1, 2019 from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_5

@@ Line 22: / Line 22: @@
 ===Summary===
-For colleagues that are not familiar with the field of biology, many parts of iDog would be difficult to use. However, most dog owners are not experts in biology. In this case, I would highly reccommend the DogPD sub-database to them. Basic information about dog breeds can be found, and the feasibility of use makes this information very easy access. Additionally, this resource is one of the best resources for colleagues looking to purchase or adopt a dog. With the credibility of this database and its contents, the searching the phenotype database for certain breeds is one of the best ways to determine what type of dog to own depending on the type of household and type of owner.<br><br>
+For colleagues that are not familiar with the field of biology, many parts of iDog would be difficult to use. However, certain parts of the database are easy that are beneficial for dog owners, veterinarians, and the average person. The DogPD sub-database would easier to navigate for people who are not proficient in biology or genetics. Basic information about dog breeds can be found, and the feasibility of use makes this information very easy access. Additionally, this resource is one of the best resources for colleagues looking to purchase or adopt a dog. With the credibility of this database and its contents, searching the phenotype database for certain breeds is one of the best ways to determining what type of dog to own depending on the type of household and type of owner.<br><br>
-This database seems in no was amateur. As it is a published database through a credible source, this database should not be classified as a "hobby" database.
 ===Acknowledgements===

← Older revision		Revision as of 02:55, 3 October 2019
Line 17:		Line 17:

	At the top of the page, a "Download" tab is available to download Genome data, SNP data, and Expression data. These files are available in .fa or .bam format. External software is required to convert this into a more universal format such as .zip. This makes it problematic to access the data without the proper database software. The homepage of iDog is user-friendly and organized, but it is difficult to find and understand the tutorials or the help section. All the different sub-databases are clearly labeled and linked as soon as the website is open. User-friendlies somewhat decreases within these sub-databases. Those with less experience in the field may find obtaining information is more difficult to navigate through. While some, such as the gene database, have simple search fields with optional advanced fields, others, such as DogGD, simply have a list of links to narrow down what the user is looking for. These links are very specific and it may not be intuitive for someone lacking the knowledge of biology to access. When running a query via the search fields, information is presented easily and quickly. This is assuming that the user either knows what they are searching for or and knowledgeable enough to use advanced search fields to find a set of information. iDog is unrestricted and is available to the public at no cost.		At the top of the page, a "Download" tab is available to download Genome data, SNP data, and Expression data. These files are available in .fa or .bam format. External software is required to convert this into a more universal format such as .zip. This makes it problematic to access the data without the proper database software. The homepage of iDog is user-friendly and organized, but it is difficult to find and understand the tutorials or the help section. All the different sub-databases are clearly labeled and linked as soon as the website is open. User-friendlies somewhat decreases within these sub-databases. Those with less experience in the field may find obtaining information is more difficult to navigate through. While some, such as the gene database, have simple search fields with optional advanced fields, others, such as DogGD, simply have a list of links to narrow down what the user is looking for. These links are very specific and it may not be intuitive for someone lacking the knowledge of biology to access. When running a query via the search fields, information is presented easily and quickly. This is assuming that the user either knows what they are searching for or and knowledgeable enough to use advanced search fields to find a set of information. iDog is unrestricted and is available to the public at no cost.
		+

	The general utility of it leans towards a professional style database that specializes in dogs. The database is relatively easy to navigate if you understand the information provided or have a background in biology but if you do not have a background or not understanding what you are looking for in the database then navigating becomes problematic. The database does not provide the best help or tutorials.		The general utility of it leans towards a professional style database that specializes in dogs. The database is relatively easy to navigate if you understand the information provided or have a background in biology but if you do not have a background or not understanding what you are looking for in the database then navigating becomes problematic. The database does not provide the best help or tutorials.

@@ Line 14: / Line 14: @@
 ===General utility of the database to the scientific community===
-Links are provided for the curated sub-databases on the homepage of iDog. This includes [https://bigd.big.ac.cn/idog/pages/gene/gene_search.jsp Gene and Annotation], [http://bigd.big.ac.cn/doggd DogGD], [http://bigd.big.ac.cn/dogsdv2 DogSD], [https://bigd.big.ac.cn/idog/pages/phenotype/phenotype.jsp DogPD], [https://bigd.big.ac.cn/idog/pages/expression/index.jsp DogED], [https://bigd.big.ac.cn/idog/go/geneontology.action?goacc=GO:0003674&type=1 GO Function Annotations], [https://bigd.big.ac.cn/idog/pages/doghdc/search.jsp DogHDC], and a query for [https://bigd.big.ac.cn/idog/pages/reference/reference_search.jsp Dog Literature]. These databases all have a somewhat intuitive user interface depending on the level of expertise in the field of biology and bioinformatics. However, the phenotype database is more accessible to those with little to no experience. Dog owners can search by dog breeds and obtain information about dogs such as personality traits, levels of shedding, and other general information about owning that breed of dog.<br><br>
+Links are provided for the curated sub-databases on the homepage of iDog. This includes [https://bigd.big.ac.cn/idog/pages/gene/gene_search.jsp Gene and Annotation], [http://bigd.big.ac.cn/doggd DogGD], [http://bigd.big.ac.cn/dogsdv2 DogSD], [https://bigd.big.ac.cn/idog/pages/phenotype/phenotype.jsp DogPD], [https://bigd.big.ac.cn/idog/pages/expression/index.jsp DogED], [https://bigd.big.ac.cn/idog/go/geneontology.action?goacc=GO:0003674&type=1 GO Function Annotations], [https://bigd.big.ac.cn/idog/pages/doghdc/search.jsp DogHDC], and a query for [https://bigd.big.ac.cn/idog/pages/reference/reference_search.jsp Dog Literature]. These databases all have an intuitive user interface depending on the level of expertise in the field of biology and bioinformatics, which makes it difficult to navigate if you do not have prior knowledge of what you are looking for. However, the phenotype database is more accessible to those with little to no experience. Dog owners can search by dog breeds and obtain information about dogs such as personality traits, levels of shedding, and other general information about owning that breed of dog. The information is useful to people looking to buy a dog. Other types of people to use this database would be veterinarians to be up to date with information regarding dogs.<br><br>
-At the top of the page, a "Download" tab is available to download Genome data, SNP data, and Expression data. These files are available in .fa format. External software is required to convert this into a more universal format such as .zip. The homepage of iDog is quite user-friendly. All the different sub-databases are clearly labeled and linked as soon as the website is open. User-friendlies somewhat decreases within these sub-databases. Those with less experience in the field may find obtaining information somewhat more difficult to find. While some, such as the gene database, have simple search fields with optional advanced fields, others, such as DogGD, simply have a list of links to narrow down what the user is looking for. These links are very specific and it may not be intuitive for someone lacking the knowledge of biology to access. When running a query via the search fields, information is presented easily and quickly. This is assuming that the user either knows what they are searching for or and knowledgeable enough to use advanced search fields to find a set of information. iDog is unrestricted and is available to the public at no cost.
 ===Summary===