IDog Week 5
Contents
iDog Database
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.
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 as it is a much more refined topic that pertains to only dogs. Thus, this information was curated to specifically fit the target of biological information of domestic dogs and wild canids. Although not specified, due the data obtained across many platforms to form the iDog database, it can be inferred 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 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 credibly whole. 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 owner ship of dogs being as popular as it is, biologically relevant information can be used to make medical advancements for veterinarians. As mentioned before, the accessibility of iDog for average dog owner also makes this database a great resource to gather some additional information on one's own dog.
iDog was first available to the piublic on January 17th, 2017. Since the day of publication, iDog was recieving 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 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.
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.
