Difference between revisions of "IDog Week 5"
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==Purpose== | ==Purpose== | ||
The purpose of this assignment is to become familiar with a specific database. Specifically, top-tier databases published in the Database Issue of ''Nucleic Acid Research'' were selected from. The chosen database, iDog, will be thoroughly observed and evaluated, and an oral presentation will be given on the information regarding this database. | The purpose of this assignment is to become familiar with a specific database. Specifically, top-tier databases published in the Database Issue of ''Nucleic Acid Research'' were selected from. The chosen database, iDog, will be thoroughly observed and evaluated, and an oral presentation will be given on the information regarding this database. | ||
| + | |||
| + | The general idea is to be able to visit the database and understand what are the pros and cons of the website. By selecting a particular database, iDog, we have to be able to identify the information if it is useful, whether it is accessible to the public, and is easily navigated by people who do not specialize in genetics or biology. | ||
==Database Evaluation== | ==Database Evaluation== | ||
===General information about the database=== | ===General information about the database=== | ||
| − | [https://bigd.big.ac.cn/idog/index.jsp iDog] is a database best described as a research resource for domestic dogs and wild Canids. It contains gene, genome, SNP, phenotype, ontology, disease, and expression data from smaller sub-databases (created by the same group). Additionally, iDog features online tools for genomic data visualization and analysis. iDog is a secondary source, as it is a compilation of smaller databases and information gathered from larger databases. This database differs | + | [https://bigd.big.ac.cn/idog/index.jsp iDog] is a database best described as a research resource for domestic dogs and wild Canids. It contains gene, genome, SNP, phenotype, ontology, disease, and expression data from smaller sub-databases (created by the same group). Additionally, iDog features online tools for genomic data visualization and analysis. iDog is a secondary source, as it is a compilation of smaller databases and information gathered from larger databases. This database differs it specializes on only dogs (genetics, phenotype, etc.). Thus, this information was curated to specifically fit the target of biological information regarding domestic dogs and wild canids. Although not specified, the data is obtained across multiple platforms to form the iDog database, in which infers that an electronic curation method was used to obtain the large amounts of data contained within this database. iDog is a public database maintained by the [https://bigd.big.ac.cn/about National Genomics Data Center (NGDC)] based out of China, and funding for this database is from various associations and programs of the Chinese Academy of Science. |
===Scientific quality of the database=== | ===Scientific quality of the database=== | ||
| − | iDog provides a plethora of information pertaining to dogs. With tens-of-millions of unique data, the coverage on this database is phenomenal. Being derived from smaller, previously created databases, it makes sense that this database is | + | iDog provides a plethora of information pertaining to dogs. With the tens-of-millions of unique data, the coverage on this database is phenomenal. Being derived from smaller, previously created databases, it makes sense that this database is credible. The database is specific for domestic dogs (''Canis lupus familiaris'') and wild canids, providing a great resource for the dog research community. The information contained in iDog is viable for answering a plethora of biological questions. With the vast information on genomes, SNPs, genes, and other biologically pertinent information, a researcher studying a specific breed of domestic or wild dog can easily find comparative information for their study. Additionally, even the average dog owner with little to no background of biology can search the phenotype database to gather general information about their dog. iDog's literature database is also useful for citing articles pertaining to a specific dog breed or trait for those academically writing about dogs.<br><br> |
| − | The nature of having a database about domestic and wild dogs is quite relevant. Specifically, with the domestic | + | The nature of having a database about domestic and wild dogs is quite relevant. Specifically, with the domestic ownership of dogs being as popular as it is, biologically relevant information can be used to make medical advancements for veterinarians. The accessibility of iDog, for the average dog owner, makes this database a great resource to gather some additional information on a person's dog or if you intend to look up a possible dog breed that you want to get.<br><br> |
| − | iDog was first available to the | + | iDog was first available to the public on January 17th, 2017. Since the day of publication, iDog was receiving regular updates every few months. However, there was a gap of no updates between April 9th, 2018 and June 21st, 2019, with the latter being the last published update of the database. |
| + | |||
===General utility of the database to the scientific community=== | ===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 | + | 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 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. | ||
| + | |||
| + | ===Summary=== | ||
| + | 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 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== | ||
| + | *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. | ||
| + | *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.''' | ||
| + | |||
| + | [[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) | ||
| + | |||
| + | ==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 | ||
| + | |||
| + | 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.== | ||
| + | [[Category:Journal Entry]] | ||
| + | {{marmas}} | ||
| + | {{jcowan4}} | ||
Latest revision as of 20:50, 2 October 2019
Contents
Purpose
The purpose of this assignment is to become familiar with a specific database. Specifically, top-tier databases published in the Database Issue of Nucleic Acid Research were selected from. The chosen database, iDog, will be thoroughly observed and evaluated, and an oral presentation will be given on the information regarding this database.
The general idea is to be able to visit the database and understand what are the pros and cons of the website. By selecting a particular database, iDog, we have to be able to identify the information if it is useful, whether it is accessible to the public, and is easily navigated by people who do not specialize in genetics or biology.
Database Evaluation
General information about the database
iDog is a database best described as a research resource for domestic dogs and wild Canids. It contains gene, genome, SNP, phenotype, ontology, disease, and expression data from smaller sub-databases (created by the same group). Additionally, iDog features online tools for genomic data visualization and analysis. iDog is a secondary source, as it is a compilation of smaller databases and information gathered from larger databases. This database differs it specializes on only dogs (genetics, phenotype, etc.). Thus, this information was curated to specifically fit the target of biological information regarding domestic dogs and wild canids. Although not specified, the data is obtained across multiple platforms to form the iDog database, in which infers that an electronic curation method was used to obtain the large amounts of data contained within this database. iDog is a public database maintained by the National Genomics Data Center (NGDC) based out of China, and funding for this database is from various associations and programs of the Chinese Academy of Science.
Scientific quality of the database
iDog provides a plethora of information pertaining to dogs. With the tens-of-millions of unique data, the coverage on this database is phenomenal. Being derived from smaller, previously created databases, it makes sense that this database is credible. The database is specific for domestic dogs (Canis lupus familiaris) and wild canids, providing a great resource for the dog research community. The information contained in iDog is viable for answering a plethora of biological questions. With the vast information on genomes, SNPs, genes, and other biologically pertinent information, a researcher studying a specific breed of domestic or wild dog can easily find comparative information for their study. Additionally, even the average dog owner with little to no background of biology can search the phenotype database to gather general information about their dog. iDog's literature database is also useful for citing articles pertaining to a specific dog breed or trait for those academically writing about dogs.
The nature of having a database about domestic and wild dogs is quite relevant. Specifically, with the domestic ownership of dogs being as popular as it is, biologically relevant information can be used to make medical advancements for veterinarians. The accessibility of iDog, for the average dog owner, makes this database a great resource to gather some additional information on a person's dog or if you intend to look up a possible dog breed that you want to get.
iDog was first available to the public on January 17th, 2017. Since the day of publication, iDog was receiving regular updates every few months. However, there was a gap of no updates between April 9th, 2018 and June 21st, 2019, with the latter being the last published update of the database.
General utility of the database to the scientific community
Links are provided for the curated sub-databases on the homepage of iDog. This includes Gene and Annotation, DogGD, DogSD, DogPD, DogED, GO Function Annotations, DogHDC, and a query for 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.
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.
Summary
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.
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
- 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.
- 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.
Jcowan4 (talk) 18:25, 2 October 2019 (PDT)
Marmas (talk) 21:50, 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
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
